5-91979496-T-C

Variant names:

• chr5-91979496-T-C
• rs421379

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 0.763 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.350 AC: 14514 AN: 41410

American (AMR) AF: 0.870 AC: 13184 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3101 AN: 3466

East Asian (EAS) AF: 0.957 AC: 4932 AN: 5156

South Asian (SAS) AF: 0.774 AC: 3734 AN: 4826

European-Finnish (FIN) AF: 0.936 AC: 9905 AN: 10580

Middle Eastern (MID) AF: 0.860 AC: 251 AN: 292

European-Non Finnish (NFE) AF: 0.938 AC: 63437 AN: 67634

Other (OTH) AF: 0.826 AC: 1729 AN: 2092

Alfa AF: 0.890 Hom.: 132953

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs421379; hg19: chr5-91275313;