NM_031453.4:c.469+12897G>A

Variant names:

• chr10-14654737-C-T
• rs10508480
• NM_031453.4:c.469+12897G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_031453.4(FAM107B):​c.469+12897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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]

ENSG00000236495 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM107B	NM_031453.4	c.469+12897G>A		intron_variant	Intron 2 of 4	ENST00000181796.7	NP_113641.2
FAM107B	NM_001282695.2	c.-123+12897G>A		intron_variant	Intron 2 of 5		NP_001269624.1
LOC105376429	XR_930691.4	n.221-293C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM107B	ENST00000181796.7	c.469+12897G>A		intron_variant	Intron 2 of 4	2	NM_031453.4	ENSP00000181796.2
FAM107B	ENST00000487335.5	n.469+12897G>A		intron_variant	Intron 2 of 5	1		ENSP00000420273.1
ENSG00000236495	ENST00000443282.1	n.225+771C>T		intron_variant	Intron 2 of 2	3
ENSG00000236495	ENST00000647862.1	n.197-293C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508480; hg19: chr10-14696736;