chr15-60414247-T-G

Variant names:

• chr15-60414247-T-G
• rs7174111

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 0.673 in 151,910 control chromosomes in the GnomAD database, including 35,452 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 0.67 (35452 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102088 AN: 151792 Hom.: 35412 Cov.: 30

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.673 AC: 102183 AN: 151910 Hom.: 35452 Cov.: 30 AF XY: 0.682 AC XY: 50601 AN XY: 74226

African (AFR) AF: 0.508 AC: 21002 AN: 41378

American (AMR) AF: 0.706 AC: 10759 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2410 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4829 AN: 5178

South Asian (SAS) AF: 0.830 AC: 3992 AN: 4810

European-Finnish (FIN) AF: 0.811 AC: 8559 AN: 10558

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48360 AN: 67960

Other (OTH) AF: 0.667 AC: 1405 AN: 2106

Alfa AF: 0.706 Hom.: 19579

Bravo AF: 0.656

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.52
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7174111; hg19: chr15-60706446;