8-100995473-T-C

Variant names:

• chr8-100995473-T-C
• rs1026228
• ENST00000787668.1:n.153+8136A>G

Variant summary

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

The ENST00000787668.1(ENSG00000302534):​n.153+8136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,100 control chromosomes in the GnomAD database, including 16,392 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 0.45 (16392 hom., cov: 32)
• Consequence: ENSG00000302534 ENST00000787668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 publications found

Genes affected

ENSG00000302534 (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 (AMR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302534	ENST00000787668.1	n.153+8136A>G		intron_variant	Intron 1 of 1
ENSG00000302534	ENST00000787669.1	n.168+8136A>G		intron_variant	Intron 1 of 1
ENSG00000302534	ENST00000787670.1	n.173-2980A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67946 AN: 151982 Hom.: 16405 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.447 AC: 67952 AN: 152100 Hom.: 16392 Cov.: 32 AF XY: 0.451 AC XY: 33564 AN XY: 74350

African (AFR) AF: 0.274 AC: 11357 AN: 41514

American (AMR) AF: 0.606 AC: 9252 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3087 AN: 5172

South Asian (SAS) AF: 0.540 AC: 2599 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4643 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33346 AN: 67982

Other (OTH) AF: 0.472 AC: 998 AN: 2116

Alfa AF: 0.488 Hom.: 79070

Bravo AF: 0.456

Asia WGS AF: 0.516 AC: 1795 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.081
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1026228; hg19: chr8-102007701;