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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.585 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

African (AFR) AF: 0.581 AC: 24103 AN: 41474

American (AMR) AF: 0.516 AC: 7894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3043 AN: 5176

South Asian (SAS) AF: 0.395 AC: 1900 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7160 AN: 10562

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41264 AN: 68016

Other (OTH) AF: 0.573 AC: 1207 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6741220; hg19: chr2-241822432;