ENST00000787971.1:n.683-570A>G

Variant names:

• chr6-71691700-A-G
• rs2754042
• ENST00000787971.1:n.683-570A>G

Variant summary

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

The ENST00000787971.1(ENSG00000302585):​n.683-570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,108 control chromosomes in the GnomAD database, including 50,813 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 0.82 (50813 hom., cov: 31)
• Consequence: ENSG00000302585 ENST00000787971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 2 publications found

Genes affected

ENSG00000302585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787971.1. 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
	ENSG00000302585	ENST00000787971.1		n.683-570A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123990 AN: 151990 Hom.: 50777 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.816 AC: 124080 AN: 152108 Hom.: 50813 Cov.: 31 AF XY: 0.814 AC XY: 60544 AN XY: 74354

African (AFR) AF: 0.852 AC: 35344 AN: 41506

American (AMR) AF: 0.770 AC: 11771 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2980 AN: 3472

East Asian (EAS) AF: 0.636 AC: 3282 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3787 AN: 4808

European-Finnish (FIN) AF: 0.837 AC: 8859 AN: 10582

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55474 AN: 67976

Other (OTH) AF: 0.804 AC: 1697 AN: 2112

Alfa AF: 0.815 Hom.: 25821

Bravo AF: 0.808

Asia WGS AF: 0.697 AC: 2425 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.38
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2754042; hg19: chr6-72401403;