6-32623148-G-A

Variant names:

• chr6-32623148-G-A
• rs3129763
• ENST00000843606.1:n.-25C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000843606.1(ENSG00000309733):​n.-25C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,132 control chromosomes in the GnomAD database, including 4,398 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 0.23 (4398 hom., cov: 33)
• Consequence: ENSG00000309733 ENST00000843606.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 80 publications found

Genes affected

ENSG00000309733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843606.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309733	ENST00000843606.1		n.-25C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35282 AN: 152014 Hom.: 4395 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152132 Hom.: 4398 Cov.: 33 AF XY: 0.228 AC XY: 16942 AN XY: 74370

African (AFR) AF: 0.245 AC: 10150 AN: 41462

American (AMR) AF: 0.243 AC: 3709 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.148 AC: 770 AN: 5188

South Asian (SAS) AF: 0.205 AC: 989 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1686 AN: 10592

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16237 AN: 67990

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.243 Hom.: 13495

Bravo AF: 0.238

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3129763; hg19: chr6-32590925;