8-114759725-T-C

Position:

• chr8-114759725-T-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 0.107 in 152,238 control chromosomes in the GnomAD database, including 1,475 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 0.11 (1475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16335 AN: 152120 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.107 AC: 16346 AN: 152238 Hom.: 1475 Cov.: 32 AF XY: 0.108 AC XY: 8037 AN XY: 74430

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.0454

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.0802 Hom.: 146

Bravo AF: 0.117

Asia WGS AF: 0.0860 AC: 298 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.63
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2045155; hg19: chr8-115771954;