chr8-134013917-A-G

Variant names:

• chr8-134013917-A-G
• rs7819815
• ENST00000846273.1:n.269+5844T>C

Variant summary

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

The ENST00000846273.1(ENSG00000309969):​n.269+5844T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,128 control chromosomes in the GnomAD database, including 2,165 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 0.16 (2165 hom., cov: 32)
• Consequence: ENSG00000309969 ENST00000846273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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.269+5844T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23659 AN: 152012 Hom.: 2164 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.156 AC: 23665 AN: 152128 Hom.: 2165 Cov.: 32 AF XY: 0.151 AC XY: 11246 AN XY: 74386

African (AFR) AF: 0.263 AC: 10900 AN: 41470

American (AMR) AF: 0.112 AC: 1714 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3472

East Asian (EAS) AF: 0.149 AC: 774 AN: 5178

South Asian (SAS) AF: 0.0699 AC: 337 AN: 4820

European-Finnish (FIN) AF: 0.0750 AC: 795 AN: 10604

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8307 AN: 67990

Other (OTH) AF: 0.160 AC: 336 AN: 2104

Alfa AF: 0.134 Hom.: 1975

Bravo AF: 0.167

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7819815; hg19: chr8-135026160;