chr5-23627559-G-T

Position:

• chr5-23627559-G-T

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 0.651 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.23627559G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.658

Alfa AF: 0.743 Hom.: 28253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402426; hg19: chr5-23627668;