rs180040

chr15-97027933-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 0.845 in 152,148 control chromosomes in the GnomAD database, including 54,908 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 0.85 (54908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128483 AN: 152030 Hom.: 54848 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.845 AC: 128605 AN: 152148 Hom.: 54908 Cov.: 32 AF XY: 0.841 AC XY: 62535 AN XY: 74374

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.876

Alfa AF: 0.814 Hom.: 6340

Bravo AF: 0.864

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	3.5
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180040; hg19: chr15-97571163;