rs6989593

Variant names:

• chr8-46639634-A-G
• rs6989593
• ENST00000787002.1:n.132+22073A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-46639634-A-G
• chr8-46639634-A-T

Variant summary

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

The ENST00000787002.1(ENSG00000302462):​n.132+22073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,834 control chromosomes in the GnomAD database, including 24,385 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 0.51 (24385 hom., cov: 32)
• Consequence: ENSG00000302462 ENST00000787002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 8 publications found

Genes affected

ENSG00000302462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302462	ENST00000787002.1	n.132+22073A>G		intron_variant	Intron 1 of 3
ENSG00000302462	ENST00000787006.1	n.126+22073A>G		intron_variant	Intron 1 of 2
ENSG00000302462	ENST00000787007.1	n.126-11450A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77908 AN: 151716 Hom.: 24389 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.513 AC: 77897 AN: 151834 Hom.: 24385 Cov.: 32 AF XY: 0.510 AC XY: 37826 AN XY: 74180

African (AFR) AF: 0.144 AC: 5978 AN: 41430

American (AMR) AF: 0.555 AC: 8451 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2084 AN: 3464

East Asian (EAS) AF: 0.649 AC: 3326 AN: 5126

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4816

European-Finnish (FIN) AF: 0.641 AC: 6769 AN: 10568

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47414 AN: 67882

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.653 Hom.: 50654

Bravo AF: 0.492

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.25
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6989593; hg19: chr8-47551256;