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.

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: 0.420 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 v4.9

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;