4-80997467-C-T

Variant names:

• chr4-80997467-C-T
• rs2868079

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 0.813 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

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 (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.813 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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.827

Alfa AF: 0.877 Hom.: 27030

Bravo AF: 0.799

Asia WGS AF: 0.897 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868079; hg19: chr4-81918621;