rs2158813

chr7-155784581-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;