rs9790855

Variant names:

• chr5-78303030-C-T
• rs9790855

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 0.343 in 151,974 control chromosomes in the GnomAD database, including 9,210 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 0.34 (9210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.343 AC: 52088 AN: 151856 Hom.: 9194 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.343 AC: 52143 AN: 151974 Hom.: 9210 Cov.: 32 AF XY: 0.342 AC XY: 25414 AN XY: 74276

African (AFR) AF: 0.384 AC: 15936 AN: 41460

American (AMR) AF: 0.274 AC: 4185 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3466

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1497 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3655 AN: 10520

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22661 AN: 67950

Other (OTH) AF: 0.348 AC: 736 AN: 2114

Alfa AF: 0.340 Hom.: 24269

Bravo AF: 0.340

Asia WGS AF: 0.301 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.19
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9790855; hg19: chr5-77598854;