chr8-23667845-C-T

Position:

• chr8-23667845-C-T

Variant summary

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

The variant allele was found at a frequency of 0.487 in 151,816 control chromosomes in the GnomAD database, including 19,340 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 0.49 (19340 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23667845C>T		intergenic_region
LOC107986930	XR_001745841.2	n.583-798C>T		intron_variant
LOC107986930	XR_001745842.2	n.1205-798C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73926 AN: 151698 Hom.: 19336 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.487 AC: 73956 AN: 151816 Hom.: 19340 Cov.: 31 AF XY: 0.487 AC XY: 36140 AN XY: 74180

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.497

Alfa AF: 0.541 Hom.: 5245

Bravo AF: 0.483

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11782388; hg19: chr8-23525358;