chr5-157893268-G-A

Variant names:

• chr5-157893268-G-A
• rs1186919

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.806 in 152,172 control chromosomes in the GnomAD database, including 50,084 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 (50084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.806 AC: 122539 AN: 152054 Hom.: 50062 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.806 AC: 122614 AN: 152172 Hom.: 50084 Cov.: 32 AF XY: 0.805 AC XY: 59907 AN XY: 74402

African (AFR) AF: 0.859 AC: 35640 AN: 41490

American (AMR) AF: 0.698 AC: 10651 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2863 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2092 AN: 5182

South Asian (SAS) AF: 0.784 AC: 3779 AN: 4820

European-Finnish (FIN) AF: 0.872 AC: 9235 AN: 10596

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55713 AN: 68030

Other (OTH) AF: 0.785 AC: 1657 AN: 2110

Alfa AF: 0.803 Hom.: 155134

Bravo AF: 0.788

Asia WGS AF: 0.602 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.019
DANN	Benign	0.65
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1186919; hg19: chr5-157320276;