rs10508477

Variant names:

• chr10-14556741-G-C
• rs10508477
• NM_031453.4:c.470-26226C>G

Variant summary

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

The NM_031453.4(FAM107B):​c.470-26226C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,102 control chromosomes in the GnomAD database, including 19,533 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 0.50 (19533 hom., cov: 34)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031453.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	NM_031453.4	MANE Select	c.470-26226C>G		intron	N/A	NP_113641.2
	FAM107B	NM_001282695.2		c.-122-3354C>G		intron	N/A	NP_001269624.1	Q9H098-1
	FAM107B	NM_001282696.2		c.-122-3354C>G		intron	N/A	NP_001269625.1	Q9H098-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	ENST00000181796.7	TSL:2 MANE Select	c.470-26226C>G		intron	N/A	ENSP00000181796.2	Q9H098-2
	FAM107B	ENST00000378467.8	TSL:1	c.-122-3354C>G		intron	N/A	ENSP00000367728.4	Q9H098-1
	FAM107B	ENST00000468747.5	TSL:1	c.-56-26226C>G		intron	N/A	ENSP00000418120.1	Q9H098-1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76338 AN: 151984 Hom.: 19513 Cov.: 34

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.502 AC: 76415 AN: 152102 Hom.: 19533 Cov.: 34 AF XY: 0.507 AC XY: 37704 AN XY: 74348

African (AFR) AF: 0.423 AC: 17536 AN: 41490

American (AMR) AF: 0.441 AC: 6740 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1543 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3122 AN: 5182

South Asian (SAS) AF: 0.684 AC: 3302 AN: 4824

European-Finnish (FIN) AF: 0.554 AC: 5851 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36654 AN: 67972

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.520 Hom.: 2550

Bravo AF: 0.485

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.25
DANN	Benign	0.34
PhyloP100		-0.43
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: rs10508477; hg19: chr10-14598740;