2-21160870-A-G

Variant names:

• chr2-21160870-A-G
• rs4591370

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;