rs6741278

chr2-232537655-T-C

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 0.389 in 152,102 control chromosomes in the GnomAD database, including 12,044 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 0.39 (12044 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.389 AC: 59154 AN: 151984 Hom.: 12012 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.389 AC: 59227 AN: 152102 Hom.: 12044 Cov.: 33 AF XY: 0.393 AC XY: 29216 AN XY: 74356

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.407

Alfa AF: 0.366 Hom.: 2265

Bravo AF: 0.408

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6741278; hg19: chr2-233402365;