8-48321512-T-G

Variant names:

• chr8-48321512-T-G
• rs1027966
• ENST00000786193.1:n.319-25238T>G

Variant summary

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

The ENST00000786193.1(ENSG00000302367):​n.319-25238T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,082 control chromosomes in the GnomAD database, including 35,738 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 0.67 (35738 hom., cov: 32)
• Consequence: ENSG00000302367 ENST00000786193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• Publications: 1 publications found

Genes affected

ENSG00000302367 (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 = 0.759 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
ENSG00000302367	ENST00000786193.1	n.319-25238T>G		intron_variant	Intron 3 of 5
ENSG00000302367	ENST00000786194.1	n.236-25238T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.671 AC: 102024 AN: 151964 Hom.: 35727 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.671 AC: 102066 AN: 152082 Hom.: 35738 Cov.: 32 AF XY: 0.676 AC XY: 50232 AN XY: 74356

African (AFR) AF: 0.464 AC: 19199 AN: 41416

American (AMR) AF: 0.754 AC: 11523 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3472

East Asian (EAS) AF: 0.593 AC: 3063 AN: 5168

South Asian (SAS) AF: 0.680 AC: 3280 AN: 4826

European-Finnish (FIN) AF: 0.832 AC: 8821 AN: 10598

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51974 AN: 67996

Other (OTH) AF: 0.662 AC: 1399 AN: 2114

Alfa AF: 0.712 Hom.: 13944

Bravo AF: 0.655

Asia WGS AF: 0.592 AC: 2060 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	3.9
DANN	Benign	0.67
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1027966; hg19: chr8-49234072;