rs12442211

Positions:

• chr15-73953334-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.514 in 151,900 control chromosomes in the GnomAD database, including 20,184 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 0.51 (20184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

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: 0.514 AC: 78087 AN: 151782 Hom.: 20173 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.514 AC: 78146 AN: 151900 Hom.: 20184 Cov.: 32 AF XY: 0.518 AC XY: 38424 AN XY: 74220

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.521

Alfa AF: 0.510 Hom.: 27983

Bravo AF: 0.514

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12442211; hg19: chr15-74245675;