chr15-94714049-T-C

Position:

• chr15-94714049-T-C

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 0.735 in 152,156 control chromosomes in the GnomAD database, including 41,473 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 0.73 (41473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111720 AN: 152038 Hom.: 41422 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.735 AC: 111826 AN: 152156 Hom.: 41473 Cov.: 33 AF XY: 0.740 AC XY: 55003 AN XY: 74352

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.730

Alfa AF: 0.701 Hom.: 36351

Bravo AF: 0.747

Asia WGS AF: 0.785 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388779; hg19: chr15-95257278;