rs6543570

Variant names:

• chr2-239679472-A-G
• rs6543570

Your query was ambiguous. Multiple possible variants found:

• chr2-239679472-A-G
• chr2-239679472-A-T

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 0.4 in 152,046 control chromosomes in the GnomAD database, including 13,080 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 0.40 (13080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.400 AC: 60748 AN: 151928 Hom.: 13054 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.400 AC: 60817 AN: 152046 Hom.: 13080 Cov.: 33 AF XY: 0.409 AC XY: 30425 AN XY: 74340

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.383

Alfa AF: 0.343 Hom.: 19752

Bravo AF: 0.417

Asia WGS AF: 0.545 AC: 1896 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	0.71
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6543570; hg19: chr2-240601166;