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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.877 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

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.883

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2740208; hg19: chr20-3053634;