chr8-114107210-G-T

Position:

• chr8-114107210-G-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 0.336 in 149,700 control chromosomes in the GnomAD database, including 8,753 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 0.34 (8753 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.336 AC: 50345 AN: 149620 Hom.: 8753 Cov.: 29

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.336 AC: 50362 AN: 149700 Hom.: 8753 Cov.: 29 AF XY: 0.332 AC XY: 24235 AN XY: 72906

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.359

Alfa AF: 0.379 Hom.: 16995

Bravo AF: 0.331

Asia WGS AF: 0.304 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12675001; hg19: chr8-115119439;