chr12-76333156-T-C

Variant names:

• chr12-76333156-T-C
• rs11615969

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0341 in 152,264 control chromosomes in the GnomAD database, including 111 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 0.034 (111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0341 (5185/152264) while in subpopulation NFE AF = 0.0513 (3491/68006). AF 95% confidence interval is 0.0499. There are 111 homozygotes in GnomAd4. There are 2420 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 111 gene

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: 0.0341 AC: 5184 AN: 152146 Hom.: 110 Cov.: 31

Gnomad AFR AF: 0.00782

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0341 AC: 5185 AN: 152264 Hom.: 111 Cov.: 31 AF XY: 0.0325 AC XY: 2420 AN XY: 74464

African (AFR) AF: 0.00782 AC: 325 AN: 41560

American (AMR) AF: 0.0345 AC: 528 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4822

European-Finnish (FIN) AF: 0.0289 AC: 306 AN: 10606

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3491 AN: 68006

Other (OTH) AF: 0.0397 AC: 84 AN: 2116

Alfa AF: 0.0403 Hom.: 17

Bravo AF: 0.0342

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.84
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11615969; hg19: chr12-76726936;