5-23627559-G-T

Variant names:

• chr5-23627559-G-T
• rs1402426

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 0.651 in 151,990 control chromosomes in the GnomAD database, including 34,473 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 0.65 (34473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 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: 0.652 AC: 98956 AN: 151876 Hom.: 34482 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.651 AC: 98957 AN: 151990 Hom.: 34473 Cov.: 32 AF XY: 0.646 AC XY: 48018 AN XY: 74292

African (AFR) AF: 0.406 AC: 16816 AN: 41408

American (AMR) AF: 0.631 AC: 9629 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2832 AN: 3466

East Asian (EAS) AF: 0.529 AC: 2724 AN: 5150

South Asian (SAS) AF: 0.551 AC: 2658 AN: 4824

European-Finnish (FIN) AF: 0.770 AC: 8139 AN: 10572

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53829 AN: 67986

Other (OTH) AF: 0.658 AC: 1391 AN: 2114

Alfa AF: 0.740 Hom.: 33686

Bravo AF: 0.632

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.63
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1402426; hg19: chr5-23627668;