chr5-18469349-T-A

Position:

• chr5-18469349-T-A

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 0.73 in 151,996 control chromosomes in the GnomAD database, including 41,702 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 0.73 (41702 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.731 AC: 110990 AN: 151878 Hom.: 41695 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 111022 AN: 151996 Hom.: 41702 Cov.: 31 AF XY: 0.731 AC XY: 54338 AN XY: 74312

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.735

Alfa AF: 0.766 Hom.: 5683

Bravo AF: 0.699

Asia WGS AF: 0.640 AC: 2225 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6870006; hg19: chr5-18469458;