5-42398363-T-C

Variant names:

• chr5-42398363-T-C
• rs3764451

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 0.124 in 152,240 control chromosomes in the GnomAD database, including 1,481 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 0.12 (1481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 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: 0.124 AC: 18815 AN: 152122 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.124 AC: 18836 AN: 152240 Hom.: 1481 Cov.: 32 AF XY: 0.126 AC XY: 9356 AN XY: 74432

Gnomad4 AFR AF: 0.0357

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.121

Alfa AF: 0.125 Hom.: 317

Bravo AF: 0.114

Asia WGS AF: 0.231 AC: 804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764451; hg19: chr5-42398465;