rs7137515

Variant names:

• chr12-82068447-A-G
• rs7137515

Your query was ambiguous. Multiple possible variants found:

• chr12-82068447-A-G
• chr12-82068447-A-T

Variant summary

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

The variant allele was found at a frequency of 0.35 in 152,068 control chromosomes in the GnomAD database, including 9,792 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 0.35 (9792 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53173 AN: 151950 Hom.: 9780 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.350 AC: 53220 AN: 152068 Hom.: 9792 Cov.: 33 AF XY: 0.347 AC XY: 25827 AN XY: 74354

African (AFR) AF: 0.470 AC: 19471 AN: 41460

American (AMR) AF: 0.336 AC: 5128 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5170

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3352 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20562 AN: 67976

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.314 Hom.: 11265

Bravo AF: 0.360

Asia WGS AF: 0.289 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7137515; hg19: chr12-82462226;