15-73373165-T-G

Variant names:

• chr15-73373165-T-G
• rs4489968

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 0.197 in 152,086 control chromosomes in the GnomAD database, including 3,322 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 0.20 (3322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.197 AC: 29972 AN: 151968 Hom.: 3304 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.197 AC: 30030 AN: 152086 Hom.: 3322 Cov.: 31 AF XY: 0.197 AC XY: 14616 AN XY: 74346

African (AFR) AF: 0.289 AC: 12000 AN: 41480

American (AMR) AF: 0.184 AC: 2812 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3470

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5178

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2267 AN: 10558

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11156 AN: 67984

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.0846 Hom.: 113

Bravo AF: 0.200

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs4489968; hg19: chr15-73665506;