rs12473173

Variant names:

• chr2-195128876-C-A
• rs12473173
• XR_007088699.1:n.197-69373G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-195128876-C-A
• chr2-195128876-C-T

Variant summary

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

The XR_007088699.1(LOC105376755):​n.197-69373G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,142 control chromosomes in the GnomAD database, including 571 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 0.084 (571 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 2 publications found

Genes affected

LOC105376755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 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: 0.0845 AC: 12844 AN: 152024 Hom.: 571 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0845 AC: 12855 AN: 152142 Hom.: 571 Cov.: 32 AF XY: 0.0839 AC XY: 6238 AN XY: 74354

African (AFR) AF: 0.105 AC: 4371 AN: 41520

American (AMR) AF: 0.104 AC: 1582 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 286 AN: 3466

East Asian (EAS) AF: 0.110 AC: 570 AN: 5182

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4824

European-Finnish (FIN) AF: 0.0607 AC: 644 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4560 AN: 67944

Other (OTH) AF: 0.101 AC: 214 AN: 2116

Alfa AF: 0.0745 Hom.: 983

Bravo AF: 0.0901

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.47
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs12473173; hg19: chr2-195993600;