4-79897263-T-C

Position:

• chr4-79897263-T-C

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 0.809 in 151,866 control chromosomes in the GnomAD database, including 49,984 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 (49984 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

(HGNC:):

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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79897263T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122816 AN: 151748 Hom.: 49927 Cov.: 29

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.809 AC: 122935 AN: 151866 Hom.: 49984 Cov.: 29 AF XY: 0.812 AC XY: 60202 AN XY: 74182

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.801

Alfa AF: 0.803 Hom.: 98848

Bravo AF: 0.814

Asia WGS AF: 0.934 AC: 3246 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	0.039
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11939401; hg19: chr4-80818417;