rs1502172

Variant names:

• chr3-135516516-A-G
• rs1502172
• XR_001740926.1:n.-138T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-135516516-A-G
• chr3-135516516-A-T

Variant summary

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

The XR_924527.4(LOC105374122):​n.-138T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,836 control chromosomes in the GnomAD database, including 25,651 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 0.56 (25651 hom., cov: 31)
• Consequence: LOC105374122 XR_924527.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 5 publications found

Genes affected

LOC105374122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.665 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: 0.563 AC: 85347 AN: 151718 Hom.: 25634 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.562 AC: 85407 AN: 151836 Hom.: 25651 Cov.: 31 AF XY: 0.559 AC XY: 41426 AN XY: 74172

African (AFR) AF: 0.337 AC: 13940 AN: 41370

American (AMR) AF: 0.675 AC: 10306 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2376 AN: 3466

East Asian (EAS) AF: 0.668 AC: 3437 AN: 5142

South Asian (SAS) AF: 0.553 AC: 2658 AN: 4804

European-Finnish (FIN) AF: 0.524 AC: 5518 AN: 10536

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45004 AN: 67942

Other (OTH) AF: 0.614 AC: 1296 AN: 2112

Alfa AF: 0.636 Hom.: 101021

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.70
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1502172; hg19: chr3-135235358;