rs2034222

Variant names:

• chr5-13681650-G-A
• rs2034222

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 0.511 in 151,872 control chromosomes in the GnomAD database, including 20,017 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 0.51 (20017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 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: 0.511 AC: 77477 AN: 151756 Hom.: 20003 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.511 AC: 77546 AN: 151872 Hom.: 20017 Cov.: 32 AF XY: 0.506 AC XY: 37547 AN XY: 74222

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.518

Alfa AF: 0.513 Hom.: 2872

Bravo AF: 0.510

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2034222; hg19: chr5-13681759;