rs6989209

Variant names:

• chr8-131111367-G-A
• rs6989209
• ENST00000745365.1:n.652-18512G>A

Variant summary

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

The ENST00000745365.1(ENSG00000297096):​n.652-18512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,152 control chromosomes in the GnomAD database, including 627 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 0.089 (627 hom., cov: 32)
• Consequence: ENSG00000297096 ENST00000745365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 2 publications found

Genes affected

ENSG00000297096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375760	XR_007061183.1	n.332-18512G>A		intron_variant	Intron 3 of 5
LOC105375760	XR_928653.3	n.194-18512G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297096	ENST00000745365.1	n.652-18512G>A		intron_variant	Intron 2 of 3
ENSG00000297096	ENST00000745366.1	n.211-18512G>A		intron_variant	Intron 2 of 5
ENSG00000297096	ENST00000745367.1	n.212-18512G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 13523 AN: 152032 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0892 AC: 13566 AN: 152152 Hom.: 627 Cov.: 32 AF XY: 0.0894 AC XY: 6653 AN XY: 74386

African (AFR) AF: 0.0976 AC: 4050 AN: 41498

American (AMR) AF: 0.108 AC: 1658 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3470

East Asian (EAS) AF: 0.0982 AC: 506 AN: 5154

South Asian (SAS) AF: 0.107 AC: 515 AN: 4826

European-Finnish (FIN) AF: 0.0687 AC: 727 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5414 AN: 68016

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0852 Hom.: 321

Bravo AF: 0.0946

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.023
DANN	Benign	0.45
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6989209; hg19: chr8-132123614;