chr5-23319063-G-C

Variant names:

• chr5-23319063-G-C
• rs1366454

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 0.154 in 151,650 control chromosomes in the GnomAD database, including 1,937 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 0.15 (1937 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 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: 0.154 AC: 23343 AN: 151532 Hom.: 1932 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.154 AC: 23366 AN: 151650 Hom.: 1937 Cov.: 32 AF XY: 0.158 AC XY: 11708 AN XY: 74088

African (AFR) AF: 0.146 AC: 6058 AN: 41390

American (AMR) AF: 0.180 AC: 2742 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 629 AN: 3464

East Asian (EAS) AF: 0.137 AC: 709 AN: 5160

South Asian (SAS) AF: 0.365 AC: 1751 AN: 4794

European-Finnish (FIN) AF: 0.149 AC: 1559 AN: 10442

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9476 AN: 67876

Other (OTH) AF: 0.173 AC: 364 AN: 2102

Alfa AF: 0.0555 Hom.: 59

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.69
DANN	Benign	0.52
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1366454; hg19: chr5-23319172;