rs10492802

Variant names:

• chr16-26370009-T-C
• rs10492802

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 0.193 in 152,094 control chromosomes in the GnomAD database, including 3,296 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 0.19 (3296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.193 AC: 29359 AN: 151978 Hom.: 3290 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.193 AC: 29404 AN: 152094 Hom.: 3296 Cov.: 32 AF XY: 0.191 AC XY: 14208 AN XY: 74364

African (AFR) AF: 0.303 AC: 12563 AN: 41464

American (AMR) AF: 0.113 AC: 1733 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3468

East Asian (EAS) AF: 0.0477 AC: 247 AN: 5176

South Asian (SAS) AF: 0.190 AC: 913 AN: 4800

European-Finnish (FIN) AF: 0.165 AC: 1743 AN: 10576

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11147 AN: 68016

Other (OTH) AF: 0.173 AC: 366 AN: 2110

Alfa AF: 0.180 Hom.: 334

Bravo AF: 0.191

Asia WGS AF: 0.135 AC: 472 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	0.34
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10492802; hg19: chr16-26381330;