rs11178997

Positions:

• chr12-71938373-T-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0945

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.100

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11178997; hg19: chr12-72332153;