5-155037420-G-T

Variant names:

• chr5-155037420-G-T
• rs286628

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 0.467 in 150,464 control chromosomes in the GnomAD database, including 18,225 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 0.47 (18225 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.467 AC: 70255 AN: 150342 Hom.: 18236 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.467 AC: 70243 AN: 150464 Hom.: 18225 Cov.: 31 AF XY: 0.465 AC XY: 34203 AN XY: 73510

African (AFR) AF: 0.248 AC: 9957 AN: 40122

American (AMR) AF: 0.420 AC: 6389 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2033 AN: 3452

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5154

South Asian (SAS) AF: 0.513 AC: 2464 AN: 4800

European-Finnish (FIN) AF: 0.560 AC: 5895 AN: 10524

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40166 AN: 67890

Other (OTH) AF: 0.495 AC: 1037 AN: 2094

Alfa AF: 0.498 Hom.: 2595

Bravo AF: 0.436

Asia WGS AF: 0.434 AC: 1509 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	3.2
DANN	Benign	0.36
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs286628; hg19: chr5-154416980;