8-11486618-C-T

Variant names:

• chr8-11486618-C-T
• rs2618473

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.423 AC: 17509 AN: 41422

American (AMR) AF: 0.482 AC: 7356 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3464

East Asian (EAS) AF: 0.721 AC: 3720 AN: 5162

South Asian (SAS) AF: 0.350 AC: 1685 AN: 4814

European-Finnish (FIN) AF: 0.275 AC: 2896 AN: 10544

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17756 AN: 67958

Other (OTH) AF: 0.328 AC: 693 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.60
PhyloP100		-0.35
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2618473; hg19: chr8-11344127;