4-80997467-C-T

Variant names:

• chr4-80997467-C-T
• rs2868079

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 0.813 in 152,108 control chromosomes in the GnomAD database, including 51,572 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 0.81 (51572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123533 AN: 151990 Hom.: 51539 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.813 AC: 123610 AN: 152108 Hom.: 51572 Cov.: 32 AF XY: 0.815 AC XY: 60599 AN XY: 74346

African (AFR) AF: 0.598 AC: 24770 AN: 41452

American (AMR) AF: 0.878 AC: 13407 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2675 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4852 AN: 5158

South Asian (SAS) AF: 0.894 AC: 4307 AN: 4820

European-Finnish (FIN) AF: 0.919 AC: 9744 AN: 10606

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61075 AN: 68008

Other (OTH) AF: 0.827 AC: 1747 AN: 2112

Alfa AF: 0.874 Hom.: 30148

Bravo AF: 0.799

Asia WGS AF: 0.897 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2868079; hg19: chr4-81918621;