rs892839

Variant names:

• chr2-238497805-G-A
• rs892839

Your query was ambiguous. Multiple possible variants found:

• chr2-238497805-G-A
• chr2-238497805-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.134 in 152,124 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.137 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: 0.134 AC: 20335 AN: 152006 Hom.: 1478 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.134 AC: 20358 AN: 152124 Hom.: 1484 Cov.: 31 AF XY: 0.135 AC XY: 10020 AN XY: 74354

African (AFR) AF: 0.137 AC: 5695 AN: 41496

American (AMR) AF: 0.0909 AC: 1391 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3468

East Asian (EAS) AF: 0.131 AC: 676 AN: 5156

South Asian (SAS) AF: 0.0973 AC: 468 AN: 4812

European-Finnish (FIN) AF: 0.196 AC: 2071 AN: 10582

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9442 AN: 67994

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.126 Hom.: 2406

Bravo AF: 0.127

Asia WGS AF: 0.119 AC: 417 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	2.3
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs892839; hg19: chr2-239406446;