rs9665534

Variant names:

• chr10-14675100-T-G
• rs9665534
• NM_031453.4:c.412-7409A>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.412-7409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,980 control chromosomes in the GnomAD database, including 31,158 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 0.63 (31158 hom., cov: 30)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM107B	NM_031453.4	c.412-7409A>C		intron_variant	Intron 1 of 4	ENST00000181796.7	NP_113641.2
FAM107B	NM_001282695.2	c.-180-7409A>C		intron_variant	Intron 1 of 5		NP_001269624.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM107B	ENST00000181796.7	c.412-7409A>C		intron_variant	Intron 1 of 4	2	NM_031453.4	ENSP00000181796.2
FAM107B	ENST00000487335.5	n.412-7409A>C		intron_variant	Intron 1 of 5	1		ENSP00000420273.1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95736 AN: 151862 Hom.: 31159 Cov.: 30

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.630 AC: 95777 AN: 151980 Hom.: 31158 Cov.: 30 AF XY: 0.639 AC XY: 47488 AN XY: 74294

African (AFR) AF: 0.455 AC: 18849 AN: 41394

American (AMR) AF: 0.677 AC: 10325 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2112 AN: 3466

East Asian (EAS) AF: 0.617 AC: 3192 AN: 5172

South Asian (SAS) AF: 0.728 AC: 3510 AN: 4822

European-Finnish (FIN) AF: 0.803 AC: 8496 AN: 10578

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47317 AN: 67970

Other (OTH) AF: 0.596 AC: 1260 AN: 2114

Alfa AF: 0.674 Hom.: 59071

Bravo AF: 0.612

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-1.5
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: rs9665534; hg19: chr10-14717099;