ENST00000641764.1:n.126+279T>C

Variant names:

• chr8-8719132-A-G
• rs9329165
• ENST00000641764.1:n.126+279T>C

Variant summary

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

The ENST00000641764.1(ENSG00000284717):​n.126+279T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,004 control chromosomes in the GnomAD database, including 5,678 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 (5678 hom., cov: 32)
• Consequence: ENSG00000284717 ENST00000641764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 5 publications found

Genes affected

ENSG00000284717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641764.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284717	ENST00000641764.1		n.126+279T>C		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.660+4398T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40212 AN: 151886 Hom.: 5663 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.265 AC: 40259 AN: 152004 Hom.: 5678 Cov.: 32 AF XY: 0.273 AC XY: 20250 AN XY: 74286

African (AFR) AF: 0.211 AC: 8757 AN: 41482

American (AMR) AF: 0.306 AC: 4666 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2262 AN: 5152

South Asian (SAS) AF: 0.406 AC: 1952 AN: 4806

European-Finnish (FIN) AF: 0.347 AC: 3659 AN: 10548

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17283 AN: 67974

Other (OTH) AF: 0.256 AC: 540 AN: 2106

Alfa AF: 0.202 Hom.: 625

Bravo AF: 0.259

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9329165; hg19: chr8-8576642;