3-73701842-A-G

Variant names:

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

Variant summary

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

The XR_001740755.1(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_001740755.1 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.

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

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 v4.3

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;