rs9665534

chr10-14675100-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• 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/exons	MANE	UniProt
FAM107B	NM_031453.4	c.412-7409A>C		intron_variant		ENST00000181796.7
FAM107B	NM_001282695.2	c.-180-7409A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7	c.412-7409A>C		intron_variant		2	NM_031453.4
FAM107B	ENST00000487335.5	c.412-7409A>C		intron_variant, NMD_transcript_variant		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

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.596

Alfa AF: 0.680 Hom.: 47765

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9665534; hg19: chr10-14717099;