rs10499276

chr6-153988673-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0869

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.0411

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.118 Hom.: 1529

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499276; hg19: chr6-154309808;