8-12878878-T-C

Variant names:

• chr8-12878878-T-C
• rs2948369
• ENST00000838107.1:n.238-14921A>G

Variant summary

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

The ENST00000838107.1(ENSG00000309058):​n.238-14921A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,166 control chromosomes in the GnomAD database, including 55,356 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 0.84 (55356 hom., cov: 32)
• Consequence: ENSG00000309058 ENST00000838107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 1 publications found

Genes affected

ENSG00000309058 (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 (SAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379289	XR_949509.3	n.652+6880T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309058	ENST00000838107.1	n.238-14921A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127990 AN: 152048 Hom.: 55333 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.842 AC: 128066 AN: 152166 Hom.: 55356 Cov.: 32 AF XY: 0.845 AC XY: 62858 AN XY: 74398

African (AFR) AF: 0.624 AC: 25873 AN: 41462

American (AMR) AF: 0.868 AC: 13261 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3281 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4245 AN: 5186

South Asian (SAS) AF: 0.936 AC: 4510 AN: 4820

European-Finnish (FIN) AF: 0.974 AC: 10340 AN: 10616

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63633 AN: 68020

Other (OTH) AF: 0.857 AC: 1811 AN: 2114

Alfa AF: 0.912 Hom.: 32612

Bravo AF: 0.821

Asia WGS AF: 0.865 AC: 3010 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	0.64
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2948369; hg19: chr8-12736387;