rs6546442

Variant names:

• chr2-68856986-G-A
• rs6546442

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 0.134 in 152,154 control chromosomes in the GnomAD database, including 2,172 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 0.13 (2172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.134 AC: 20378 AN: 152036 Hom.: 2163 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0619

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.134 AC: 20420 AN: 152154 Hom.: 2172 Cov.: 32 AF XY: 0.132 AC XY: 9808 AN XY: 74420

African (AFR) AF: 0.302 AC: 12513 AN: 41442

American (AMR) AF: 0.111 AC: 1705 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3472

East Asian (EAS) AF: 0.124 AC: 642 AN: 5170

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4826

European-Finnish (FIN) AF: 0.0518 AC: 549 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4271 AN: 68034

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0779 Hom.: 359

Bravo AF: 0.146

Asia WGS AF: 0.112 AC: 391 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	1.4
DANN	Benign	0.20
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6546442; hg19: chr2-69084118;