17-44905727-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002055.5(GFAP):​c.*1620C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 156,562 control chromosomes in the GnomAD database, including 913 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 886 hom., cov: 33)
Exomes 𝑓: 0.099 ( 27 hom. )

Consequence

GFAP
NM_002055.5 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.328
Variant links:
Genes affected
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 17-44905727-G-A is Benign according to our data. Variant chr17-44905727-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 369148.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GFAPNM_002055.5 linkuse as main transcriptc.*1620C>T 3_prime_UTR_variant 9/9 ENST00000588735.3
GFAPNM_001363846.2 linkuse as main transcriptc.*1620C>T 3_prime_UTR_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GFAPENST00000588735.3 linkuse as main transcriptc.*1620C>T 3_prime_UTR_variant 9/91 NM_002055.5 P1P14136-1

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16370
AN:
152114
Hom.:
888
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0954
Gnomad AMI
AF:
0.111
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.171
Gnomad EAS
AF:
0.0897
Gnomad SAS
AF:
0.115
Gnomad FIN
AF:
0.0852
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.131
GnomAD4 exome
AF:
0.0986
AC:
427
AN:
4330
Hom.:
27
Cov.:
0
AF XY:
0.100
AC XY:
296
AN XY:
2950
show subpopulations
Gnomad4 AFR exome
AF:
0.0658
Gnomad4 AMR exome
AF:
0.0543
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.0735
Gnomad4 SAS exome
AF:
0.101
Gnomad4 FIN exome
AF:
0.0667
Gnomad4 NFE exome
AF:
0.100
Gnomad4 OTH exome
AF:
0.114
GnomAD4 genome
AF:
0.108
AC:
16370
AN:
152232
Hom.:
886
Cov.:
33
AF XY:
0.106
AC XY:
7856
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0953
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.0897
Gnomad4 SAS
AF:
0.115
Gnomad4 FIN
AF:
0.0852
Gnomad4 NFE
AF:
0.115
Gnomad4 OTH
AF:
0.130
Alfa
AF:
0.109
Hom.:
136
Bravo
AF:
0.109
Asia WGS
AF:
0.102
AC:
356
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
8.5
DANN
Benign
0.79

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: rs7049; hg19: chr17-42983095; API