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. Variant got -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

Genes affected

LOC105377164 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377164	XR_001740755.1	n.239-4511T>C		intron_variant	Intron 1 of 2
LOC105377164	XR_940966.1	n.239-4511T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.455

Alfa AF: 0.475 Hom.: 15696

Bravo AF: 0.402

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137064; hg19: chr3-73750993;