rs10499276

Variant names:

• chr6-153988673-C-T
• rs10499276

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.11 in 152,060 control chromosomes in the GnomAD database, including 1,014 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 0.11 (1014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.111 AC: 16802 AN: 151942 Hom.: 1013 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.110 AC: 16798 AN: 152060 Hom.: 1014 Cov.: 32 AF XY: 0.109 AC XY: 8125 AN XY: 74326

African (AFR) AF: 0.0869 AC: 3603 AN: 41482

American (AMR) AF: 0.0871 AC: 1331 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3470

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5168

South Asian (SAS) AF: 0.0411 AC: 198 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10552

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8714 AN: 67972

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.117 Hom.: 1906

Bravo AF: 0.102

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	21
DANN	Benign	0.78
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs10499276; hg19: chr6-154309808;