17-44903502-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001258400.2(FAM187A):​c.-328C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000841 in 1,277,138 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 3 hom. )

Consequence

FAM187A
NM_001258400.2 5_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -1.29
Variant links:
Genes affected
FAM187A (HGNC:35153): (family with sequence similarity 187 member A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
GFAP (HGNC:4235): (glial fibrillary acidic protein) This gene encodes one of the major intermediate filament proteins of mature astrocytes. It is used as a marker to distinguish astrocytes from other glial cells during development. Mutations in this gene cause Alexander disease, a rare disorder of astrocytes in the central nervous system. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
CCDC103 (HGNC:32700): (coiled-coil domain containing 103) Enables protein homodimerization activity. Involved in axonemal dynein complex assembly; cilium movement; and determination of left/right symmetry. Predicted to be located in axoneme. Predicted to be part of outer dynein arm. Implicated in primary ciliary dyskinesia 17. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM187ANM_001258400.2 linkuse as main transcriptc.-328C>T 5_prime_UTR_variant 1/1 ENST00000331733.5 NP_001245329.1
GFAPNM_002055.5 linkuse as main transcriptc.*3845G>A 3_prime_UTR_variant 9/9 ENST00000588735.3 NP_002046.1
CCDC103NM_213607.3 linkuse as main transcriptc.*685C>T 3_prime_UTR_variant 4/4 ENST00000417826.3 NP_998772.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM187AENST00000331733.5 linkuse as main transcriptc.-328C>T 5_prime_UTR_variant 1/11 NM_001258400.2 ENSP00000329499 P1
CCDC103ENST00000417826.3 linkuse as main transcriptc.*685C>T 3_prime_UTR_variant 4/41 NM_213607.3 ENSP00000391692 P1Q8IW40-1
GFAPENST00000588735.3 linkuse as main transcriptc.*3845G>A 3_prime_UTR_variant 9/91 NM_002055.5 ENSP00000466598 P1P14136-1

Frequencies

GnomAD3 genomes
AF:
0.00422
AC:
643
AN:
152194
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0152
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00143
GnomAD4 exome
AF:
0.000381
AC:
429
AN:
1124826
Hom.:
3
Cov.:
31
AF XY:
0.000352
AC XY:
188
AN XY:
533596
show subpopulations
Gnomad4 AFR exome
AF:
0.0151
Gnomad4 AMR exome
AF:
0.000424
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000351
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000306
Gnomad4 OTH exome
AF:
0.000632
GnomAD4 genome
AF:
0.00423
AC:
645
AN:
152312
Hom.:
4
Cov.:
32
AF XY:
0.00416
AC XY:
310
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0152
Gnomad4 AMR
AF:
0.000457
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00312
Hom.:
1
Bravo
AF:
0.00465
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Primary ciliary dyskinesia 17 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.82
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs539555310; hg19: chr17-42980870; API