15-78754943-G-T

Variant names:

• chr15-78754943-G-T
• rs3743068

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 0.372 in 152,040 control chromosomes in the GnomAD database, including 13,494 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 0.37 (13494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.371 AC: 56422 AN: 151922 Hom.: 13461 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.372 AC: 56508 AN: 152040 Hom.: 13494 Cov.: 32 AF XY: 0.376 AC XY: 27943 AN XY: 74302

African (AFR) AF: 0.629 AC: 26083 AN: 41454

American (AMR) AF: 0.431 AC: 6583 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3936 AN: 5166

South Asian (SAS) AF: 0.380 AC: 1830 AN: 4810

European-Finnish (FIN) AF: 0.242 AC: 2564 AN: 10592

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13578 AN: 67950

Other (OTH) AF: 0.364 AC: 770 AN: 2114

Alfa AF: 0.271 Hom.: 2743

Bravo AF: 0.401

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs3743068; hg19: chr15-79047285;