chr2-6352263-A-G

Variant names:

• chr2-6352263-A-G
• rs726342

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 0.271 in 151,942 control chromosomes in the GnomAD database, including 6,217 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 0.27 (6217 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41191 AN: 151820 Hom.: 6214 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.271 AC: 41201 AN: 151942 Hom.: 6217 Cov.: 31 AF XY: 0.273 AC XY: 20244 AN XY: 74282

African (AFR) AF: 0.133 AC: 5512 AN: 41484

American (AMR) AF: 0.303 AC: 4627 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1643 AN: 5134

South Asian (SAS) AF: 0.426 AC: 2049 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10544

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21874 AN: 67912

Other (OTH) AF: 0.303 AC: 639 AN: 2106

Alfa AF: 0.311 Hom.: 26911

Bravo AF: 0.265

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.59
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs726342; hg19: chr2-6492395;