rs7921651

Variant names:

• chr10-14618200-C-T
• rs7921651
• NM_031453.4:c.469+49434G>A

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+49434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,030 control chromosomes in the GnomAD database, including 4,637 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 0.24 (4637 hom., cov: 31)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 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.469+49434G>A		intron	N/A	NP_113641.2
	FAM107B	NM_001282695.2		c.-123+49434G>A		intron	N/A	NP_001269624.1	Q9H098-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	ENST00000181796.7	TSL:2 MANE Select	c.469+49434G>A		intron	N/A	ENSP00000181796.2	Q9H098-2
	FAM107B	ENST00000487335.5	TSL:1	n.469+49434G>A		intron	N/A	ENSP00000420273.1	F8WDH7

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36755 AN: 151912 Hom.: 4629 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.242 AC: 36809 AN: 152030 Hom.: 4637 Cov.: 31 AF XY: 0.240 AC XY: 17825 AN XY: 74322

African (AFR) AF: 0.236 AC: 9798 AN: 41454

American (AMR) AF: 0.331 AC: 5062 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3468

East Asian (EAS) AF: 0.167 AC: 865 AN: 5172

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1983 AN: 10570

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16823 AN: 67962

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.243 Hom.: 10217

Bravo AF: 0.251

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		-0.30
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: rs7921651; hg19: chr10-14660199;