rs9790879

Variant names:

• chr5-44899783-C-T
• rs9790879

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 0.541 in 152,014 control chromosomes in the GnomAD database, including 22,710 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 0.54 (22710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.541 AC: 82222 AN: 151896 Hom.: 22707 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.541 AC: 82237 AN: 152014 Hom.: 22710 Cov.: 32 AF XY: 0.538 AC XY: 39969 AN XY: 74272

African (AFR) AF: 0.453 AC: 18784 AN: 41460

American (AMR) AF: 0.531 AC: 8120 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2331 AN: 5180

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4816

European-Finnish (FIN) AF: 0.600 AC: 6323 AN: 10534

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40356 AN: 67964

Other (OTH) AF: 0.546 AC: 1150 AN: 2108

Alfa AF: 0.576 Hom.: 20870

Bravo AF: 0.531

Asia WGS AF: 0.436 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.9
DANN	Benign	0.81
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9790879; hg19: chr5-44899885;