12-6393542-T-C

Variant names:

• chr12-6393542-T-C
• rs11064160

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 0.254 in 152,188 control chromosomes in the GnomAD database, including 7,703 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 0.25 (7703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.254 AC: 38592 AN: 152070 Hom.: 7700 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.254 AC: 38621 AN: 152188 Hom.: 7703 Cov.: 32 AF XY: 0.253 AC XY: 18860 AN XY: 74406

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.255

Alfa AF: 0.147 Hom.: 2790

Bravo AF: 0.272

Asia WGS AF: 0.522 AC: 1814 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	2.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11064160; hg19: chr12-6502708;