5-91979496-T-C

Position:

• chr5-91979496-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 0.763 in 151,528 control chromosomes in the GnomAD database, including 49,171 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 0.76 (49171 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91979496T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115638 AN: 151410 Hom.: 49171 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.763 AC: 115650 AN: 151528 Hom.: 49171 Cov.: 31 AF XY: 0.766 AC XY: 56731 AN XY: 74064

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.826

Alfa AF: 0.915 Hom.: 99250

Bravo AF: 0.743

Asia WGS AF: 0.805 AC: 2784 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs421379; hg19: chr5-91275313;