12-6393542-T-C

Variant names:

• chr12-6393542-T-C
• rs11064160

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 0.254 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
• Publications: 8 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 (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

African (AFR) AF: 0.490 AC: 20317 AN: 41474

American (AMR) AF: 0.160 AC: 2440 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4075 AN: 5186

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4816

European-Finnish (FIN) AF: 0.0856 AC: 908 AN: 10610

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8256 AN: 68018

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.158 Hom.: 4242

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
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs11064160; hg19: chr12-6502708;