10-14670444-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031453.4(FAM107B):​c.412-2753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,088 control chromosomes in the GnomAD database, including 9,872 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 9872 hom., cov: 33)

Consequence

FAM107B
NM_031453.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.623
Variant links:
Genes affected
FAM107B (HGNC:23726): (family with sequence similarity 107 member B) Predicted to act upstream of or within sensory perception of sound. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM107BNM_031453.4 linkuse as main transcriptc.412-2753T>C intron_variant ENST00000181796.7 NP_113641.2
FAM107BNM_001282695.2 linkuse as main transcriptc.-180-2753T>C intron_variant NP_001269624.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM107BENST00000181796.7 linkuse as main transcriptc.412-2753T>C intron_variant 2 NM_031453.4 ENSP00000181796 Q9H098-2
FAM107BENST00000487335.5 linkuse as main transcriptc.412-2753T>C intron_variant, NMD_transcript_variant 1 ENSP00000420273

Frequencies

GnomAD3 genomes
AF:
0.357
AC:
54329
AN:
151970
Hom.:
9858
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.336
Gnomad AMI
AF:
0.478
Gnomad AMR
AF:
0.379
Gnomad ASJ
AF:
0.480
Gnomad EAS
AF:
0.411
Gnomad SAS
AF:
0.334
Gnomad FIN
AF:
0.271
Gnomad MID
AF:
0.437
Gnomad NFE
AF:
0.367
Gnomad OTH
AF:
0.413
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.358
AC:
54372
AN:
152088
Hom.:
9872
Cov.:
33
AF XY:
0.353
AC XY:
26247
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.336
Gnomad4 AMR
AF:
0.379
Gnomad4 ASJ
AF:
0.480
Gnomad4 EAS
AF:
0.411
Gnomad4 SAS
AF:
0.334
Gnomad4 FIN
AF:
0.271
Gnomad4 NFE
AF:
0.367
Gnomad4 OTH
AF:
0.412
Alfa
AF:
0.367
Hom.:
4859
Bravo
AF:
0.368
Asia WGS
AF:
0.354
AC:
1232
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.4
DANN
Benign
0.75

Splicing

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: rs1459019; hg19: chr10-14712443; API