chr8-109073637-C-T

Position:

• chr8-109073637-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 0.219 in 152,144 control chromosomes in the GnomAD database, including 3,933 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 0.22 (3933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33375 AN: 152026 Hom.: 3930 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.219 AC: 33383 AN: 152144 Hom.: 3933 Cov.: 33 AF XY: 0.219 AC XY: 16298 AN XY: 74368

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.198

Alfa AF: 0.202 Hom.: 819

Bravo AF: 0.223

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
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: rs4466373; hg19: chr8-110085866;