8-94071359-G-T

Variant names:

• chr8-94071359-G-T
• rs10096362
• ENST00000804339.1:n.80+50899G>T

Variant summary

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

The ENST00000804339.1(ENSG00000304524):​n.80+50899G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,152 control chromosomes in the GnomAD database, including 1,259 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 0.12 (1259 hom., cov: 32)
• Consequence: ENSG00000304524 ENST00000804339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 3 publications found

Genes affected

ENSG00000304524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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
ENSG00000304524	ENST00000804339.1	n.80+50899G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18577 AN: 152034 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.122 AC: 18589 AN: 152152 Hom.: 1259 Cov.: 32 AF XY: 0.125 AC XY: 9313 AN XY: 74370

African (AFR) AF: 0.0697 AC: 2894 AN: 41510

American (AMR) AF: 0.126 AC: 1928 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3470

East Asian (EAS) AF: 0.103 AC: 531 AN: 5172

South Asian (SAS) AF: 0.141 AC: 681 AN: 4828

European-Finnish (FIN) AF: 0.186 AC: 1959 AN: 10552

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9642 AN: 68000

Other (OTH) AF: 0.130 AC: 276 AN: 2116

Alfa AF: 0.131 Hom.: 1939

Bravo AF: 0.116

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0080
DANN	Benign	0.74
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10096362; hg19: chr8-95083587;