ENST00000818771.1:n.640-8841T>C

Variant names:

• chr7-95452698-T-C
• rs10240398
• ENST00000818771.1:n.640-8841T>C

Variant summary

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

The ENST00000818771.1(ENSG00000233942):​n.640-8841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,052 control chromosomes in the GnomAD database, including 32,220 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 0.64 (32220 hom., cov: 33)
• Consequence: ENSG00000233942 ENST00000818771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 4 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818771.1. 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
	ENSG00000233942	ENST00000818771.1		n.640-8841T>C		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.464-17994T>C		intron	N/A
	ENSG00000233942	ENST00000818773.1		n.554-8841T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96610 AN: 151930 Hom.: 32166 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.636 AC: 96727 AN: 152052 Hom.: 32220 Cov.: 33 AF XY: 0.640 AC XY: 47564 AN XY: 74326

African (AFR) AF: 0.802 AC: 33276 AN: 41492

American (AMR) AF: 0.643 AC: 9816 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2019 AN: 3464

East Asian (EAS) AF: 0.937 AC: 4844 AN: 5170

South Asian (SAS) AF: 0.635 AC: 3063 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6164 AN: 10566

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35674 AN: 67952

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.567 Hom.: 110898

Bravo AF: 0.652

Asia WGS AF: 0.773 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10240398; hg19: chr7-95082010;