rs276568

chr6-137101615-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.565 in 150,266 control chromosomes in the GnomAD database, including 24,956 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 0.56 (24956 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.565 AC: 84804 AN: 150148 Hom.: 24940 Cov.: 25

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.565 AC: 84850 AN: 150266 Hom.: 24956 Cov.: 25 AF XY: 0.569 AC XY: 41695 AN XY: 73236

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.568

Alfa AF: 0.616 Hom.: 39492

Bravo AF: 0.553

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276568; hg19: chr6-137422752; COSMIC: COSV69427936;