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_001740926.1(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_001740926.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374122	XR_001740926.1	n.-138T>C		upstream_gene_variant
LOC105374122	XR_002959651.2	n.-138T>C		upstream_gene_variant
LOC105374122	XR_007096111.1	n.-138T>C		upstream_gene_variant

Ensembl

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

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 v4.3

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;