rs180040

Variant names:

• chr15-97027933-T-C
• rs180040

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;