chr6-95519536-T-C

Variant names:

• chr6-95519536-T-C
• rs2380220
• ENST00000839529.1:n.-167A>G

Variant summary

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

The ENST00000839529.1(ENSG00000309204):​n.-167A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,176 control chromosomes in the GnomAD database, including 55,155 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 0.85 (55155 hom., cov: 33)
• Consequence: ENSG00000309204 ENST00000839529.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 6 publications found

Genes affected

ENSG00000309204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839529.1. 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
	ENSG00000309204	ENST00000839529.1		n.-167A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128977 AN: 152060 Hom.: 55109 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.848 AC: 129080 AN: 152176 Hom.: 55155 Cov.: 33 AF XY: 0.842 AC XY: 62631 AN XY: 74368

African (AFR) AF: 0.929 AC: 38580 AN: 41548

American (AMR) AF: 0.699 AC: 10680 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2869 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4888 AN: 5142

South Asian (SAS) AF: 0.829 AC: 3997 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8240 AN: 10594

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56996 AN: 67992

Other (OTH) AF: 0.837 AC: 1767 AN: 2112

Alfa AF: 0.836 Hom.: 33407

Bravo AF: 0.846

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.42
DANN	Benign	0.47
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2380220; hg19: chr6-95967412;