5-18327496-C-T

Variant names:

• chr5-18327496-C-T
• rs314025

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 0.109 in 151,818 control chromosomes in the GnomAD database, including 1,308 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 0.11 (1308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 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: 0.110 AC: 16615 AN: 151700 Hom.: 1309 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.109 AC: 16619 AN: 151818 Hom.: 1308 Cov.: 31 AF XY: 0.110 AC XY: 8181 AN XY: 74208

African (AFR) AF: 0.158 AC: 6551 AN: 41442

American (AMR) AF: 0.143 AC: 2174 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1983 AN: 5154

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4820

European-Finnish (FIN) AF: 0.0244 AC: 259 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0655 AC: 4445 AN: 67832

Other (OTH) AF: 0.125 AC: 263 AN: 2100

Alfa AF: 0.0871 Hom.: 1071

Bravo AF: 0.122

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.54
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs314025; hg19: chr5-18327605;