chr8-133989625-T-C

Variant names:

• chr8-133989625-T-C
• rs1119729
• ENST00000846273.1:n.431+1279A>G

Variant summary

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

The ENST00000846273.1(ENSG00000309969):​n.431+1279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,950 control chromosomes in the GnomAD database, including 8,225 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 0.32 (8225 hom., cov: 31)
• Consequence: ENSG00000309969 ENST00000846273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 1 publications found

Genes affected

ENSG00000309969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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
ENSG00000309969	ENST00000846273.1	n.431+1279A>G		intron_variant	Intron 3 of 3
ENSG00000309969	ENST00000846274.1	n.275+1279A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47833 AN: 151832 Hom.: 8220 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.315 AC: 47874 AN: 151950 Hom.: 8225 Cov.: 31 AF XY: 0.309 AC XY: 22922 AN XY: 74268

African (AFR) AF: 0.437 AC: 18089 AN: 41436

American (AMR) AF: 0.224 AC: 3412 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5168

South Asian (SAS) AF: 0.214 AC: 1025 AN: 4798

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19920 AN: 67956

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.274 Hom.: 3044

Bravo AF: 0.311

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1119729; hg19: chr8-135001868;