rs2137064

Variant names:

• chr3-73701842-A-G
• rs2137064
• XR_001740755.1:n.239-4511T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-73701842-A-G
• chr3-73701842-A-T

Variant summary

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

The XR_940966.1(LOC105377164):​n.239-4511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,068 control chromosomes in the GnomAD database, including 13,829 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 0.41 (13829 hom., cov: 32)
• Consequence: LOC105377164 XR_940966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 3 publications found

Genes affected

LOC105377164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62489 AN: 151948 Hom.: 13814 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.411 AC: 62542 AN: 152068 Hom.: 13829 Cov.: 32 AF XY: 0.415 AC XY: 30848 AN XY: 74348

African (AFR) AF: 0.233 AC: 9685 AN: 41494

American (AMR) AF: 0.457 AC: 6985 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1988 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2228 AN: 5158

South Asian (SAS) AF: 0.498 AC: 2397 AN: 4814

European-Finnish (FIN) AF: 0.496 AC: 5233 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32528 AN: 67980

Other (OTH) AF: 0.455 AC: 961 AN: 2112

Alfa AF: 0.465 Hom.: 20332

Bravo AF: 0.402

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs2137064; hg19: chr3-73750993;