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

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031453.4(FAM107B):​c.469+12897G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,244 control chromosomes in the GnomAD database, including 61,949 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 0.90 (61949 hom., cov: 32)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM107B	NM_031453.4	c.469+12897G>C		intron_variant	Intron 2 of 4	ENST00000181796.7	NP_113641.2
FAM107B	NM_001282695.2	c.-123+12897G>C		intron_variant	Intron 2 of 5		NP_001269624.1
LOC105376429	XR_930691.4	n.221-293C>G		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>C		intron_variant	Intron 2 of 4	2	NM_031453.4	ENSP00000181796.2
FAM107B	ENST00000487335.5	n.469+12897G>C		intron_variant	Intron 2 of 5	1		ENSP00000420273.1
ENSG00000236495	ENST00000443282.1	n.225+771C>G		intron_variant	Intron 2 of 2	3
ENSG00000236495	ENST00000647862.1	n.197-293C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136990 AN: 152126 Hom.: 61909 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.900 AC: 137083 AN: 152244 Hom.: 61949 Cov.: 32 AF XY: 0.899 AC XY: 66942 AN XY: 74434

African (AFR) AF: 0.876 AC: 36400 AN: 41536

American (AMR) AF: 0.847 AC: 12946 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3147 AN: 3472

East Asian (EAS) AF: 0.716 AC: 3701 AN: 5166

South Asian (SAS) AF: 0.827 AC: 3995 AN: 4828

European-Finnish (FIN) AF: 0.965 AC: 10234 AN: 10610

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63695 AN: 68024

Other (OTH) AF: 0.904 AC: 1909 AN: 2112

Alfa AF: 0.921 Hom.: 8022

Bravo AF: 0.887

Asia WGS AF: 0.739 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.36
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10508480; hg19: chr10-14696736;