12-96414139-T-C

Variant names:

• chr12-96414139-T-C
• rs11108495

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 0.376 in 151,916 control chromosomes in the GnomAD database, including 10,926 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 0.38 (10926 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.376 AC: 57051 AN: 151798 Hom.: 10926 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.376 AC: 57073 AN: 151916 Hom.: 10926 Cov.: 31 AF XY: 0.375 AC XY: 27842 AN XY: 74276

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.396

Alfa AF: 0.370 Hom.: 13219

Bravo AF: 0.387

Asia WGS AF: 0.421 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11108495; hg19: chr12-96807917;