rs4341893

Positions:

• chr2-20935817-A-G
• chr2-20935817-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 0.722 in 152,042 control chromosomes in the GnomAD database, including 40,113 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 0.72 (40113 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109719 AN: 151924 Hom.: 40064 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.722 AC: 109826 AN: 152042 Hom.: 40113 Cov.: 31 AF XY: 0.720 AC XY: 53492 AN XY: 74302

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.767

Alfa AF: 0.687 Hom.: 74648

Bravo AF: 0.730

Asia WGS AF: 0.716 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4341893; hg19: chr2-21135577;