15-72998562-T-C

Variant names:

• chr15-72998562-T-C
• rs7174900

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 0.112 in 152,198 control chromosomes in the GnomAD database, including 1,918 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 0.11 (1918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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: 0.112 AC: 17004 AN: 152080 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.112 AC: 17056 AN: 152198 Hom.: 1918 Cov.: 32 AF XY: 0.110 AC XY: 8158 AN XY: 74420

African (AFR) AF: 0.291 AC: 12072 AN: 41468

American (AMR) AF: 0.0535 AC: 818 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3470

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5180

South Asian (SAS) AF: 0.0386 AC: 186 AN: 4824

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0399 AC: 2713 AN: 68016

Other (OTH) AF: 0.0956 AC: 202 AN: 2114

Alfa AF: 0.0446 Hom.: 187

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.053
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7174900; hg19: chr15-73290903;