rs10498516

Variant names:

• chr14-64642608-A-C
• rs10498516

Your query was ambiguous. Multiple possible variants found:

• chr14-64642608-A-C
• chr14-64642608-A-T

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 0.149 in 152,242 control chromosomes in the GnomAD database, including 1,857 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 0.15 (1857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.149 AC: 22707 AN: 152124 Hom.: 1859 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.149 AC: 22706 AN: 152242 Hom.: 1857 Cov.: 32 AF XY: 0.151 AC XY: 11251 AN XY: 74420

African (AFR) AF: 0.101 AC: 4187 AN: 41566

American (AMR) AF: 0.107 AC: 1636 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 498 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5178

South Asian (SAS) AF: 0.175 AC: 845 AN: 4828

European-Finnish (FIN) AF: 0.211 AC: 2236 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11579 AN: 67996

Other (OTH) AF: 0.161 AC: 341 AN: 2116

Alfa AF: 0.163 Hom.: 9100

Bravo AF: 0.139

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10498516; hg19: chr14-65109326;