rs12911814

Positions:

• chr15-78621642-A-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 0.0307 in 151,352 control chromosomes in the GnomAD database, including 105 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 0.031 (105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0307 (4641/151352) while in subpopulation NFE AF= 0.0494 (3353/67916). AF 95% confidence interval is 0.048. There are 105 homozygotes in gnomad4. There are 2151 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 105 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4640 AN: 151236 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000208

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0293

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

GnomAD4 genome AF: 0.0307 AC: 4641 AN: 151352 Hom.: 105 Cov.: 32 AF XY: 0.0291 AC XY: 2151 AN XY: 73980

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.000209

Gnomad4 SAS AF: 0.0150

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0290

Alfa AF: 0.0374 Hom.: 15

Bravo AF: 0.0295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.89
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12911814; hg19: chr15-78913984;