rs1877252

Variant names:

• chr3-73678389-T-C
• rs1877252
• XR_001740755.1:n.387A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-73678389-T-C
• chr3-73678389-T-G

Variant summary

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

The XR_001740755.1(LOC105377164):​n.387A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,044 control chromosomes in the GnomAD database, including 14,721 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 0.42 (14721 hom., cov: 31)
• Consequence: LOC105377164 XR_001740755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377164	XR_001740755.1	n.387A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63806 AN: 151926 Hom.: 14716 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.420 AC: 63823 AN: 152044 Hom.: 14721 Cov.: 31 AF XY: 0.421 AC XY: 31268 AN XY: 74308

African (AFR) AF: 0.212 AC: 8814 AN: 41498

American (AMR) AF: 0.463 AC: 7065 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2883 AN: 5148

South Asian (SAS) AF: 0.477 AC: 2293 AN: 4808

European-Finnish (FIN) AF: 0.495 AC: 5229 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34667 AN: 67972

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.448 Hom.: 2791

Bravo AF: 0.407

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs1877252; hg19: chr3-73727540;