ENST00000766995.1:n.822+2206T>C

Variant names:

• chr8-52772301-T-C
• rs7822058
• ENST00000766995.1:n.822+2206T>C

Variant summary

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

The ENST00000766995.1(ENSG00000288818):​n.822+2206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,222 control chromosomes in the GnomAD database, including 61,069 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 0.90 (61069 hom., cov: 32)
• Consequence: ENSG00000288818 ENST00000766995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 6 publications found

Genes affected

ENSG00000288818 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766995.1. 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
	ENSG00000288818	ENST00000766995.1		n.822+2206T>C		intron	N/A
	ENSG00000288818	ENST00000766996.1		n.807+2206T>C		intron	N/A
	ENSG00000288818	ENST00000766997.1		n.804+2206T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136217 AN: 152104 Hom.: 61006 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.896 AC: 136339 AN: 152222 Hom.: 61069 Cov.: 32 AF XY: 0.898 AC XY: 66806 AN XY: 74430

African (AFR) AF: 0.901 AC: 37394 AN: 41514

American (AMR) AF: 0.919 AC: 14051 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3470

East Asian (EAS) AF: 0.958 AC: 4967 AN: 5184

South Asian (SAS) AF: 0.919 AC: 4430 AN: 4820

European-Finnish (FIN) AF: 0.864 AC: 9164 AN: 10602

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60245 AN: 68024

Other (OTH) AF: 0.899 AC: 1901 AN: 2114

Alfa AF: 0.891 Hom.: 129568

Bravo AF: 0.900

Asia WGS AF: 0.934 AC: 3248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.67
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7822058; hg19: chr8-53684861;