12-71938373-T-A

Variant names:

• chr12-71938373-T-A
• rs11178997

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 0.117 in 152,254 control chromosomes in the GnomAD database, including 1,302 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 0.12 (1302 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17712 AN: 152138 Hom.: 1294 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.117 AC: 17760 AN: 152254 Hom.: 1302 Cov.: 32 AF XY: 0.117 AC XY: 8694 AN XY: 74438

African (AFR) AF: 0.212 AC: 8787 AN: 41534

American (AMR) AF: 0.0945 AC: 1446 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3472

East Asian (EAS) AF: 0.167 AC: 866 AN: 5178

South Asian (SAS) AF: 0.113 AC: 545 AN: 4826

European-Finnish (FIN) AF: 0.0761 AC: 807 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0721 AC: 4904 AN: 68030

Other (OTH) AF: 0.100 AC: 211 AN: 2110

Alfa AF: 0.0801 Hom.: 306

Bravo AF: 0.122

Asia WGS AF: 0.164 AC: 570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		-0.14
PromoterAI		0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11178997; hg19: chr12-72332153;