rs2158813

Variant names:

• chr7-155784581-C-T
• rs2158813

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 0.805 in 152,258 control chromosomes in the GnomAD database, including 50,022 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 0.81 (50022 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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: 0.805 AC: 122490 AN: 152140 Hom.: 49961 Cov.: 33

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.805 AC: 122609 AN: 152258 Hom.: 50022 Cov.: 33 AF XY: 0.808 AC XY: 60114 AN XY: 74430

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.774

Alfa AF: 0.748 Hom.: 44117

Bravo AF: 0.814

Asia WGS AF: 0.907 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2158813; hg19: chr7-155577275;