ENST00000788564.1:n.107-315G>A

Variant names:

• chr6-32791520-G-A
• rs2857161
• ENST00000788564.1:n.107-315G>A

Variant summary

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

The ENST00000788564.1(ENSG00000302653):​n.107-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,878 control chromosomes in the GnomAD database, including 32,524 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 0.65 (32524 hom., cov: 30)
• Consequence: ENSG00000302653 ENST00000788564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 22 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302653	ENST00000788564.1		n.107-315G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99167 AN: 151760 Hom.: 32504 Cov.: 30

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.653 AC: 99228 AN: 151878 Hom.: 32524 Cov.: 30 AF XY: 0.658 AC XY: 48799 AN XY: 74212

African (AFR) AF: 0.662 AC: 27418 AN: 41386

American (AMR) AF: 0.631 AC: 9631 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2236 AN: 3468

East Asian (EAS) AF: 0.736 AC: 3796 AN: 5160

South Asian (SAS) AF: 0.723 AC: 3478 AN: 4808

European-Finnish (FIN) AF: 0.703 AC: 7410 AN: 10548

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42992 AN: 67936

Other (OTH) AF: 0.650 AC: 1372 AN: 2110

Alfa AF: 0.647 Hom.: 78383

Bravo AF: 0.647

Asia WGS AF: 0.739 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.40
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2857161; hg19: chr6-32759297;