rs6741220

Variant names:

• chr2-240883015-A-G
• rs6741220

Your query was ambiguous. Multiple possible variants found:

• chr2-240883015-A-G
• chr2-240883015-A-T

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 0.585 in 152,112 control chromosomes in the GnomAD database, including 26,411 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 0.59 (26411 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.585 AC: 88992 AN: 151994 Hom.: 26381 Cov.: 34

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.585 AC: 89059 AN: 152112 Hom.: 26411 Cov.: 34 AF XY: 0.581 AC XY: 43231 AN XY: 74354

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.573

Alfa AF: 0.556 Hom.: 4819

Bravo AF: 0.577

Asia WGS AF: 0.491 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6741220; hg19: chr2-241822432;