chr5-42398363-T-C

Variant names:

• chr5-42398363-T-C
• rs3764451

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 0.124 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0357 AC: 1484 AN: 41568

American (AMR) AF: 0.116 AC: 1773 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1765 AN: 5170

South Asian (SAS) AF: 0.139 AC: 669 AN: 4830

European-Finnish (FIN) AF: 0.203 AC: 2155 AN: 10598

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10251 AN: 67998

Other (OTH) AF: 0.121 AC: 256 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs3764451; hg19: chr5-42398465;