8-52772301-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375835	XR_001745898.2	n.886+2206T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288818	ENST00000766995.1	n.822+2206T>C		intron_variant	Intron 4 of 5
ENSG00000288818	ENST00000766996.1	n.807+2206T>C		intron_variant	Intron 4 of 4
ENSG00000288818	ENST00000766997.1	n.804+2206T>C		intron_variant	Intron 4 of 4

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 v4.3

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;