chr8-10849291-C-T

Position:

• chr8-10849291-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 0.179 in 152,102 control chromosomes in the GnomAD database, including 2,523 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 0.18 (2523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.179 AC: 27218 AN: 151982 Hom.: 2519 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.179 AC: 27240 AN: 152102 Hom.: 2523 Cov.: 31 AF XY: 0.177 AC XY: 13126 AN XY: 74348

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.190

Alfa AF: 0.190 Hom.: 3630

Bravo AF: 0.175

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469557; hg19: chr8-10706801;