rs1834502

Variant names:

• chr3-139931400-A-G
• rs1834502

Your query was ambiguous. Multiple possible variants found:

• chr3-139931400-A-G
• chr3-139931400-A-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 0.891 in 152,248 control chromosomes in the GnomAD database, including 61,184 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 0.89 (61184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.891 AC: 135568 AN: 152130 Hom.: 61148 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.891 AC: 135658 AN: 152248 Hom.: 61184 Cov.: 32 AF XY: 0.896 AC XY: 66686 AN XY: 74438

African (AFR) AF: 0.737 AC: 30598 AN: 41496

American (AMR) AF: 0.940 AC: 14380 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3324 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.990 AC: 4778 AN: 4824

European-Finnish (FIN) AF: 0.957 AC: 10156 AN: 10616

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64182 AN: 68044

Other (OTH) AF: 0.917 AC: 1939 AN: 2114

Alfa AF: 0.935 Hom.: 41224

Bravo AF: 0.883

Asia WGS AF: 0.976 AC: 3394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1834502; hg19: chr3-139650242;