rs7512140

Variant names:

• chr1-161493811-G-A
• rs7512140
• XR_922214.3:n.1903+192G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-161493811-G-A
• chr1-161493811-G-C

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,070 control chromosomes in the GnomAD database, including 25,061 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 0.57 (25061 hom., cov: 33)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 9 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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: 0.569 AC: 86412 AN: 151952 Hom.: 25056 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.569 AC: 86469 AN: 152070 Hom.: 25061 Cov.: 33 AF XY: 0.565 AC XY: 41983 AN XY: 74334

African (AFR) AF: 0.543 AC: 22510 AN: 41472

American (AMR) AF: 0.604 AC: 9226 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1287 AN: 5184

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4816

European-Finnish (FIN) AF: 0.584 AC: 6164 AN: 10558

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41549 AN: 67978

Other (OTH) AF: 0.564 AC: 1192 AN: 2114

Alfa AF: 0.582 Hom.: 4203

Bravo AF: 0.571

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7512140; hg19: chr1-161463601;