rs6741278

Variant names:

• chr2-232537655-T-C
• rs6741278

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;