rs726342

chr2-6352263-A-G

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 0.271 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.271 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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.303

Alfa AF: 0.323 Hom.: 17033

Bravo AF: 0.265

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726342; hg19: chr2-6492395;