5-52600620-A-G

Variant names:

• chr5-52600620-A-G
• rs350436

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 0.353 in 151,792 control chromosomes in the GnomAD database, including 11,139 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 0.35 (11139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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: 0.354 AC: 53625 AN: 151676 Hom.: 11137 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.353 AC: 53635 AN: 151792 Hom.: 11139 Cov.: 31 AF XY: 0.353 AC XY: 26180 AN XY: 74116

African (AFR) AF: 0.132 AC: 5470 AN: 41474

American (AMR) AF: 0.352 AC: 5351 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1683 AN: 5116

South Asian (SAS) AF: 0.294 AC: 1417 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5140 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31263 AN: 67876

Other (OTH) AF: 0.376 AC: 792 AN: 2106

Alfa AF: 0.423 Hom.: 19464

Bravo AF: 0.336

Asia WGS AF: 0.287 AC: 1002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs350436; hg19: chr5-51896454;