rs2740208

Variant names:

• chr20-3072988-A-C
• rs2740208

Your query was ambiguous. Multiple possible variants found:

• chr20-3072988-A-C
• chr20-3072988-A-G
• chr20-3072988-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 0.877 in 152,176 control chromosomes in the GnomAD database, including 58,960 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 0.88 (58960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133412 AN: 152058 Hom.: 58898 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.877 AC: 133533 AN: 152176 Hom.: 58960 Cov.: 32 AF XY: 0.876 AC XY: 65175 AN XY: 74378

African (AFR) AF: 0.971 AC: 40358 AN: 41562

American (AMR) AF: 0.891 AC: 13636 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3074 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4850 AN: 5138

South Asian (SAS) AF: 0.935 AC: 4518 AN: 4830

European-Finnish (FIN) AF: 0.784 AC: 8303 AN: 10592

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56031 AN: 67978

Other (OTH) AF: 0.883 AC: 1863 AN: 2110

Alfa AF: 0.843 Hom.: 8347

Bravo AF: 0.890

Asia WGS AF: 0.957 AC: 3330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.73
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2740208; hg19: chr20-3053634;