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. The variant received -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
• Publications: 9 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 (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

African (AFR) AF: 0.462 AC: 19161 AN: 41440

American (AMR) AF: 0.536 AC: 8190 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5176

South Asian (SAS) AF: 0.449 AC: 2160 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3557 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21420 AN: 67974

Other (OTH) AF: 0.383 AC: 809 AN: 2114

Alfa AF: 0.350 Hom.: 43009

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6543570; hg19: chr2-240601166;