8-139247296-C-T

Variant names:

• chr8-139247296-C-T
• rs11783351

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 0.351 in 152,004 control chromosomes in the GnomAD database, including 10,274 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 (10274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53384 AN: 151886 Hom.: 10264 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.351 AC: 53409 AN: 152004 Hom.: 10274 Cov.: 32 AF XY: 0.356 AC XY: 26471 AN XY: 74292

African (AFR) AF: 0.190 AC: 7895 AN: 41478

American (AMR) AF: 0.461 AC: 7032 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4824

European-Finnish (FIN) AF: 0.463 AC: 4887 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28381 AN: 67944

Other (OTH) AF: 0.331 AC: 698 AN: 2106

Alfa AF: 0.385 Hom.: 18979

Bravo AF: 0.342

Asia WGS AF: 0.277 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.58
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11783351; hg19: chr8-140259539;