rs4591370

chr2-21160870-A-Gchr2-21160870-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 0.756 in 152,106 control chromosomes in the GnomAD database, including 44,196 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 0.76 (44196 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.756 AC: 114935 AN: 151988 Hom.: 44164 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.756 AC: 115020 AN: 152106 Hom.: 44196 Cov.: 31 AF XY: 0.759 AC XY: 56414 AN XY: 74366

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.757

Alfa AF: 0.759 Hom.: 8545

Bravo AF: 0.753

Asia WGS AF: 0.917 AC: 3187 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	0.80
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4591370; hg19: chr2-21383742;