chr8-24924127-C-T

Variant names:

• chr8-24924127-C-T
• rs1379356
• ENST00000781717.1:n.222+463G>A

Variant summary

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

The ENST00000781717.1(ENSG00000301773):​n.222+463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 152,178 control chromosomes in the GnomAD database, including 600 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 0.080 (600 hom., cov: 32)
• Consequence: ENSG00000301773 ENST00000781717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268023	XR_002956698.2	n.121+463G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301773	ENST00000781717.1	n.222+463G>A		intron_variant	Intron 2 of 2
ENSG00000301773	ENST00000781718.1	n.294+463G>A		intron_variant	Intron 2 of 3
ENSG00000301773	ENST00000781719.1	n.137-3192G>A		intron_variant	Intron 1 of 2
ENSG00000301773	ENST00000781720.1	n.298+463G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12103 AN: 152060 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0795 AC: 12105 AN: 152178 Hom.: 600 Cov.: 32 AF XY: 0.0769 AC XY: 5721 AN XY: 74410

African (AFR) AF: 0.119 AC: 4958 AN: 41492

American (AMR) AF: 0.0726 AC: 1109 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0668 AC: 322 AN: 4820

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10598

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0726 AC: 4940 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0474 Hom.: 49

Bravo AF: 0.0872

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.1
DANN	Benign	0.77
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1379356; hg19: chr8-24781640;