chr15-73953334-G-A

Variant names:

• chr15-73953334-G-A
• rs12442211

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.506 AC: 20956 AN: 41414

American (AMR) AF: 0.531 AC: 8120 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1757 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3334 AN: 5162

South Asian (SAS) AF: 0.601 AC: 2897 AN: 4820

European-Finnish (FIN) AF: 0.505 AC: 5334 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34125 AN: 67872

Other (OTH) AF: 0.521 AC: 1101 AN: 2112

Alfa AF: 0.509 Hom.: 38617

Bravo AF: 0.514

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs12442211; hg19: chr15-74245675;