8-92683627-T-C

Variant names:

• chr8-92683627-T-C
• rs7820107
• ENST00000744035.1:n.190-8429A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000744035.1(FLJ46284):​n.190-8429A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,244 control chromosomes in the GnomAD database, including 1,608 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 0.098 (1608 hom., cov: 32)
• Consequence: FLJ46284 ENST00000744035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 1 publications found

Genes affected

FLJ46284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101926956	NR_188017.1	n.*177T>C		downstream_gene_variant
LOC101926956	NR_188018.1	n.*177T>C		downstream_gene_variant
LOC101926956	NR_188019.1	n.*177T>C		downstream_gene_variant
LOC101926956	NR_188020.1	n.*177T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLJ46284	ENST00000744035.1	n.190-8429A>G		intron_variant	Intron 2 of 2
FLJ46284	ENST00000744049.1	n.255-8429A>G		intron_variant	Intron 3 of 3
ENSG00000253177	ENST00000745064.1	n.641+1184T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14857 AN: 152126 Hom.: 1605 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0977 AC: 14875 AN: 152244 Hom.: 1608 Cov.: 32 AF XY: 0.0924 AC XY: 6880 AN XY: 74446

African (AFR) AF: 0.270 AC: 11207 AN: 41510

American (AMR) AF: 0.0559 AC: 854 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.00932 AC: 45 AN: 4826

European-Finnish (FIN) AF: 0.0171 AC: 182 AN: 10626

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2236 AN: 68022

Other (OTH) AF: 0.0770 AC: 163 AN: 2116

Alfa AF: 0.0917 Hom.: 207

Bravo AF: 0.108

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	9.4
DANN	Benign	0.82
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs7820107; hg19: chr8-93695855;