15-78418424-C-T

Variant names:

• chr15-78418424-C-T
• rs7183034

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.56 (23664 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 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: 0.564 AC: 78736 AN: 139592 Hom.: 23609 Cov.: 19

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.564 AC: 78845 AN: 139702 Hom.: 23664 Cov.: 19 AF XY: 0.566 AC XY: 38143 AN XY: 67446

African (AFR) AF: 0.772 AC: 28085 AN: 36400

American (AMR) AF: 0.575 AC: 8019 AN: 13940

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1713 AN: 3360

East Asian (EAS) AF: 0.816 AC: 3651 AN: 4476

South Asian (SAS) AF: 0.471 AC: 1987 AN: 4216

European-Finnish (FIN) AF: 0.535 AC: 4862 AN: 9092

Middle Eastern (MID) AF: 0.585 AC: 165 AN: 282

European-Non Finnish (NFE) AF: 0.443 AC: 28852 AN: 65138

Other (OTH) AF: 0.558 AC: 1082 AN: 1940

Alfa AF: 0.482 Hom.: 28355

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.51
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7183034; hg19: chr15-78710766;