chr8-23961174-G-C

Position:

• chr8-23961174-G-C

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 0.124 in 152,164 control chromosomes in the GnomAD database, including 1,219 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 0.12 (1219 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23961174G>C		intergenic_region
LOC107986931	XR_001745844.1	n.138+42406G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18787 AN: 152046 Hom.: 1215 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.124 AC: 18802 AN: 152164 Hom.: 1219 Cov.: 32 AF XY: 0.123 AC XY: 9134 AN XY: 74368

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.134

Alfa AF: 0.138 Hom.: 830

Bravo AF: 0.121

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7833268; hg19: chr8-23818687;