rs10508477

chr10-14556741-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107B	NM_031453.4	c.470-26226C>G		intron_variant		ENST00000181796.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7	c.470-26226C>G		intron_variant		2	NM_031453.4

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

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.497

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.25
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508477; hg19: chr10-14598740;