rs11615969

Positions:

• chr12-76333156-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 111 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00782

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.0397

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11615969; hg19: chr12-76726936;