rs434363

Variant names:

• chr5-117636821-A-T
• rs434363

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 0.466 in 152,128 control chromosomes in the GnomAD database, including 20,903 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 (20903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.466 AC: 70847 AN: 152012 Hom.: 20862 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.466 AC: 70942 AN: 152128 Hom.: 20903 Cov.: 33 AF XY: 0.460 AC XY: 34185 AN XY: 74370

African (AFR) AF: 0.837 AC: 34747 AN: 41530

American (AMR) AF: 0.315 AC: 4813 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3468

East Asian (EAS) AF: 0.0412 AC: 213 AN: 5174

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4824

European-Finnish (FIN) AF: 0.318 AC: 3363 AN: 10582

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23629 AN: 67958

Other (OTH) AF: 0.447 AC: 946 AN: 2114

Alfa AF: 0.432 Hom.: 2059

Bravo AF: 0.478

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.49
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs434363; hg19: chr5-116972516;