rs359457

Variant names:

• chr5-173852839-C-T
• rs359457

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.583 in 151,922 control chromosomes in the GnomAD database, including 26,304 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 0.58 (26304 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.583 AC: 88533 AN: 151804 Hom.: 26280 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.583 AC: 88601 AN: 151922 Hom.: 26304 Cov.: 31 AF XY: 0.577 AC XY: 42827 AN XY: 74190

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.624

Alfa AF: 0.570 Hom.: 56177

Bravo AF: 0.581

Asia WGS AF: 0.561 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359457; hg19: chr5-173279842; COSMIC: COSV60233946;