10-14546602-T-G

Position:

• chr10-14546602-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031453.4(FAM107B):​c.470-16087A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,142 control chromosomes in the GnomAD database, including 49,329 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 0.80 (49329 hom., cov: 32)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107B	NM_031453.4	c.470-16087A>C		intron_variant		ENST00000181796.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7	c.470-16087A>C		intron_variant		2	NM_031453.4

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121736 AN: 152024 Hom.: 49286 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.811

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.801 AC: 121833 AN: 152142 Hom.: 49329 Cov.: 32 AF XY: 0.803 AC XY: 59744 AN XY: 74402

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.813

Alfa AF: 0.831 Hom.: 10864

Bravo AF: 0.783

Asia WGS AF: 0.871 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.27

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

Other links and lift over

dbSNP: rs7079377; hg19: chr10-14588601;