8-24924127-C-T

Variant names:

• chr8-24924127-C-T
• rs1379356
• XR_002956698.2:n.121+463G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002956698.2(LOC112268023):​n.121+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: LOC112268023 XR_002956698.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

LOC112268023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0726

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0668

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.102

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1379356; hg19: chr8-24781640;