rs2740208

chr20-3072988-A-Cchr20-3072988-A-Gchr20-3072988-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;