rs12905014

Positions:

• chr15-92340610-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 0.0236 in 152,364 control chromosomes in the GnomAD database, including 56 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 0.024 (56 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0236 (3599/152364) while in subpopulation NFE AF= 0.0343 (2335/68030). AF 95% confidence interval is 0.0332. There are 56 homozygotes in gnomad4. There are 1686 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 56 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: 0.0236 AC: 3600 AN: 152246 Hom.: 56 Cov.: 33

Gnomad AFR AF: 0.00622

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0173

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0236 AC: 3599 AN: 152364 Hom.: 56 Cov.: 33 AF XY: 0.0226 AC XY: 1686 AN XY: 74518

Gnomad4 AFR AF: 0.00620

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00849

Gnomad4 FIN AF: 0.0173

Gnomad4 NFE AF: 0.0343

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0303 Hom.: 19

Bravo AF: 0.0252

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12905014; hg19: chr15-92883840;