rs495998

Variant names:

• chr10-95585932-A-C
• rs495998

Variant summary

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

The variant allele was found at a frequency of 0.394 in 152,056 control chromosomes in the GnomAD database, including 14,445 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 0.39 (14445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59974 AN: 151938 Hom.: 14447 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.394 AC: 59972 AN: 152056 Hom.: 14445 Cov.: 31 AF XY: 0.393 AC XY: 29231 AN XY: 74318

African (AFR) AF: 0.107 AC: 4431 AN: 41492

American (AMR) AF: 0.508 AC: 7751 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3466

East Asian (EAS) AF: 0.519 AC: 2684 AN: 5168

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5398 AN: 10546

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35496 AN: 67984

Other (OTH) AF: 0.367 AC: 776 AN: 2112

Alfa AF: 0.434 Hom.: 2118

Bravo AF: 0.386

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.67
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs495998; hg19: chr10-97345689;