8-8643812-T-G

Variant names:

• chr8-8643812-T-G
• rs7013418
• ENST00000690140.1:n.309-10974T>G

Variant summary

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

The ENST00000690140.1(ENSG00000289622):​n.309-10974T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,994 control chromosomes in the GnomAD database, including 5,377 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 0.26 (5377 hom., cov: 31)
• Consequence: ENSG00000289622 ENST00000690140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 6 publications found

Genes affected

ENSG00000289622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690140.1. 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
	ENSG00000289622	ENST00000690140.1		n.309-10974T>G		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.661-13545A>C		intron	N/A
	ENSG00000289622	ENST00000765710.1		n.149-10974T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39669 AN: 151876 Hom.: 5374 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.261 AC: 39705 AN: 151994 Hom.: 5377 Cov.: 31 AF XY: 0.265 AC XY: 19698 AN XY: 74282

African (AFR) AF: 0.282 AC: 11692 AN: 41428

American (AMR) AF: 0.172 AC: 2628 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1742 AN: 5170

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3718 AN: 10548

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17219 AN: 67956

Other (OTH) AF: 0.226 AC: 477 AN: 2108

Alfa AF: 0.250 Hom.: 19332

Bravo AF: 0.252

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs7013418; hg19: chr8-8501322;