rs5008499

chr6-18044947-C-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 0.165 in 152,154 control chromosomes in the GnomAD database, including 2,348 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 0.16 (2348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25044 AN: 152036 Hom.: 2339 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.165 AC: 25077 AN: 152154 Hom.: 2348 Cov.: 32 AF XY: 0.169 AC XY: 12556 AN XY: 74394

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.174

Alfa AF: 0.168 Hom.: 3733

Bravo AF: 0.169

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5008499; hg19: chr6-18045178;