chr8-24926467-C-T

Variant names:

• chr8-24926467-C-T
• rs196854
• ENST00000781717.1:n.106-1761G>A

Variant summary

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

The ENST00000781717.1(ENSG00000301773):​n.106-1761G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,248 control chromosomes in the GnomAD database, including 60,397 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 0.89 (60397 hom., cov: 32)
• Consequence: ENSG00000301773 ENST00000781717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 1 publications found

Genes affected

ENSG00000301773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
ENSG00000301773	ENST00000781717.1	n.106-1761G>A		intron_variant	Intron 1 of 2
ENSG00000301773	ENST00000781718.1	n.178-1761G>A		intron_variant	Intron 1 of 3
ENSG00000301773	ENST00000781719.1	n.137-5532G>A		intron_variant	Intron 1 of 2
ENSG00000301773	ENST00000781720.1	n.178-1757G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135428 AN: 152130 Hom.: 60353 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.890 AC: 135530 AN: 152248 Hom.: 60397 Cov.: 32 AF XY: 0.890 AC XY: 66236 AN XY: 74426

African (AFR) AF: 0.920 AC: 38236 AN: 41546

American (AMR) AF: 0.904 AC: 13834 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3097 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5095 AN: 5180

South Asian (SAS) AF: 0.915 AC: 4401 AN: 4808

European-Finnish (FIN) AF: 0.833 AC: 8829 AN: 10594

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59081 AN: 68028

Other (OTH) AF: 0.894 AC: 1888 AN: 2112

Alfa AF: 0.876 Hom.: 9191

Bravo AF: 0.900

Asia WGS AF: 0.931 AC: 3235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.25
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs196854; hg19: chr8-24783980;