6-32790617-G-A

Variant names:

• chr6-32790617-G-A
• rs7758736
• ENST00000788564.1:n.13G>A

Variant summary

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

The ENST00000788564.1(ENSG00000302653):​n.13G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,104 control chromosomes in the GnomAD database, including 1,641 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 0.14 (1641 hom., cov: 31)
• Consequence: ENSG00000302653 ENST00000788564.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 39 publications found

Genes affected

ENSG00000302653 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788564.1. 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
	ENSG00000302653	ENST00000788564.1		n.13G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21322 AN: 151986 Hom.: 1640 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0716

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.140 AC: 21319 AN: 152104 Hom.: 1641 Cov.: 31 AF XY: 0.138 AC XY: 10263 AN XY: 74346

African (AFR) AF: 0.102 AC: 4231 AN: 41496

American (AMR) AF: 0.129 AC: 1965 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.0231 AC: 120 AN: 5184

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4820

European-Finnish (FIN) AF: 0.171 AC: 1808 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11767 AN: 67952

Other (OTH) AF: 0.141 AC: 298 AN: 2114

Alfa AF: 0.162 Hom.: 8056

Bravo AF: 0.133

Asia WGS AF: 0.0680 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.59
DANN	Benign	0.74
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7758736; hg19: chr6-32758394;