5-150845315-G-A

Variant names:

• chr5-150845315-G-A
• rs4958842

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 0.132 in 152,142 control chromosomes in the GnomAD database, including 1,766 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 0.13 (1766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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: 0.132 AC: 20137 AN: 152022 Hom.: 1765 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.132 AC: 20145 AN: 152142 Hom.: 1766 Cov.: 32 AF XY: 0.134 AC XY: 9941 AN XY: 74390

African (AFR) AF: 0.207 AC: 8608 AN: 41488

American (AMR) AF: 0.121 AC: 1851 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2003 AN: 5140

South Asian (SAS) AF: 0.130 AC: 625 AN: 4822

European-Finnish (FIN) AF: 0.0813 AC: 862 AN: 10608

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5230 AN: 67994

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.101 Hom.: 127

Bravo AF: 0.142

Asia WGS AF: 0.221 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs4958842; hg19: chr5-150224877;