4-59196967-G-T

Variant names:

• chr4-59196967-G-T
• rs9312080

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.693 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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.692

Alfa AF: 0.594 Hom.: 1848

Bravo AF: 0.686

Asia WGS AF: 0.722 AC: 2509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312080; hg19: chr4-60062685;