15-78754943-G-T

Variant names:

• chr15-78754943-G-T
• rs3743068

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.371 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

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.364

Alfa AF: 0.269 Hom.: 1691

Bravo AF: 0.401

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3743068; hg19: chr15-79047285;