chr15-68733708-C-T

Variant names:

• chr15-68733708-C-T
• rs7172123

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 0.76 in 151,810 control chromosomes in the GnomAD database, including 47,027 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 0.76 (47027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 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: 0.760 AC: 115362 AN: 151694 Hom.: 47043 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.760 AC: 115375 AN: 151810 Hom.: 47027 Cov.: 32 AF XY: 0.765 AC XY: 56805 AN XY: 74224

African (AFR) AF: 0.434 AC: 17943 AN: 41334

American (AMR) AF: 0.812 AC: 12383 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3468

East Asian (EAS) AF: 0.774 AC: 3981 AN: 5144

South Asian (SAS) AF: 0.835 AC: 4011 AN: 4806

European-Finnish (FIN) AF: 0.945 AC: 10010 AN: 10588

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61317 AN: 67920

Other (OTH) AF: 0.779 AC: 1638 AN: 2104

Alfa AF: 0.851 Hom.: 173848

Bravo AF: 0.734

Asia WGS AF: 0.785 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7172123; hg19: chr15-69026047;