rs7138288

Variant names:

• chr12-84599792-T-A
• rs7138288

Your query was ambiguous. Multiple possible variants found:

• chr12-84599792-T-A
• chr12-84599792-T-G

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 0.211 in 152,108 control chromosomes in the GnomAD database, including 3,690 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 0.21 (3690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.211 AC: 32006 AN: 151990 Hom.: 3682 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.211 AC: 32050 AN: 152108 Hom.: 3690 Cov.: 32 AF XY: 0.208 AC XY: 15432 AN XY: 74366

African (AFR) AF: 0.285 AC: 11824 AN: 41496

American (AMR) AF: 0.206 AC: 3134 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5166

South Asian (SAS) AF: 0.139 AC: 669 AN: 4828

European-Finnish (FIN) AF: 0.145 AC: 1535 AN: 10602

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12370 AN: 67986

Other (OTH) AF: 0.197 AC: 416 AN: 2114

Alfa AF: 0.182 Hom.: 330

Bravo AF: 0.223

Asia WGS AF: 0.243 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.37
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7138288; hg19: chr12-84993571;