4-59196967-G-T

Variant names:

• chr4-59196967-G-T
• rs9312080

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 0.693 in 151,972 control chromosomes in the GnomAD database, including 36,735 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 0.69 (36735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.763 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: 0.693 AC: 105196 AN: 151854 Hom.: 36679 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.693 AC: 105308 AN: 151972 Hom.: 36735 Cov.: 32 AF XY: 0.693 AC XY: 51499 AN XY: 74262

African (AFR) AF: 0.770 AC: 31900 AN: 41434

American (AMR) AF: 0.618 AC: 9410 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3138 AN: 5158

South Asian (SAS) AF: 0.723 AC: 3484 AN: 4818

European-Finnish (FIN) AF: 0.694 AC: 7331 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45317 AN: 67984

Other (OTH) AF: 0.692 AC: 1461 AN: 2112

Alfa AF: 0.605 Hom.: 2056

Bravo AF: 0.686

Asia WGS AF: 0.722 AC: 2509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9312080; hg19: chr4-60062685;