chr8-100798263-T-C

Position:

• chr8-100798263-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 0.13 in 152,158 control chromosomes in the GnomAD database, including 1,901 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 0.13 (1901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.129 AC: 19656 AN: 152040 Hom.: 1889 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.130 AC: 19716 AN: 152158 Hom.: 1901 Cov.: 32 AF XY: 0.133 AC XY: 9881 AN XY: 74396

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.0566

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.123

Alfa AF: 0.102 Hom.: 191

Bravo AF: 0.148

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
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: rs10808365; hg19: chr8-101810491;