15-101157777-T-C

Position:

• chr15-101157777-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 0.877 in 152,260 control chromosomes in the GnomAD database, including 58,756 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 0.88 (58756 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101157777T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133382 AN: 152142 Hom.: 58722 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.877 AC: 133472 AN: 152260 Hom.: 58756 Cov.: 34 AF XY: 0.878 AC XY: 65339 AN XY: 74444

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.882

Alfa AF: 0.903 Hom.: 86996

Bravo AF: 0.871

Asia WGS AF: 0.876 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1809180; hg19: chr15-101697982;