15-74050989-A-G

Variant names:

• chr15-74050989-A-G
• rs723434

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 0.19 in 152,054 control chromosomes in the GnomAD database, including 2,909 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 0.19 (2909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28837 AN: 151936 Hom.: 2905 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.190 AC: 28854 AN: 152054 Hom.: 2909 Cov.: 32 AF XY: 0.192 AC XY: 14273 AN XY: 74340

African (AFR) AF: 0.193 AC: 8020 AN: 41464

American (AMR) AF: 0.281 AC: 4296 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1621 AN: 5160

South Asian (SAS) AF: 0.163 AC: 784 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1678 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11229 AN: 67962

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.176 Hom.: 4167

Bravo AF: 0.200

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs723434; hg19: chr15-74343330; COSMIC: COSV51454962;