chr8-11486618-C-T

Position:

• chr8-11486618-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 0.346 in 151,954 control chromosomes in the GnomAD database, including 10,169 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 0.35 (10169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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 (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.345 AC: 52408 AN: 151836 Hom.: 10134 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.346 AC: 52501 AN: 151954 Hom.: 10169 Cov.: 31 AF XY: 0.351 AC XY: 26028 AN XY: 74250

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.328

Alfa AF: 0.307 Hom.: 1047

Bravo AF: 0.370

Asia WGS AF: 0.561 AC: 1949 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	0.88
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2618473; hg19: chr8-11344127;