chr8-83073061-C-T

Variant names:

• chr8-83073061-C-T
• rs4739919

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 0.888 in 152,260 control chromosomes in the GnomAD database, including 60,165 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 0.89 (60165 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.888 AC: 135121 AN: 152140 Hom.: 60119 Cov.: 33

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.888 AC: 135224 AN: 152260 Hom.: 60165 Cov.: 33 AF XY: 0.889 AC XY: 66163 AN XY: 74444

African (AFR) AF: 0.905 AC: 37642 AN: 41572

American (AMR) AF: 0.872 AC: 13325 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4348 AN: 5158

South Asian (SAS) AF: 0.855 AC: 4123 AN: 4822

European-Finnish (FIN) AF: 0.933 AC: 9903 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60274 AN: 68030

Other (OTH) AF: 0.881 AC: 1858 AN: 2110

Alfa AF: 0.881 Hom.: 31083

Bravo AF: 0.884

Asia WGS AF: 0.869 AC: 3022 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	1.8
DANN	Benign	0.35
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4739919; hg19: chr8-83985296;