chr5-175885707-G-A

Variant names:

• chr5-175885707-G-A
• rs9313730

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 0.54 in 152,088 control chromosomes in the GnomAD database, including 22,404 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 (22404 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.540 AC: 82067 AN: 151970 Hom.: 22378 Cov.: 33

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.540 AC: 82137 AN: 152088 Hom.: 22404 Cov.: 33 AF XY: 0.543 AC XY: 40386 AN XY: 74308

African (AFR) AF: 0.571 AC: 23683 AN: 41482

American (AMR) AF: 0.537 AC: 8211 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2609 AN: 5176

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4820

European-Finnish (FIN) AF: 0.663 AC: 6997 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35400 AN: 67992

Other (OTH) AF: 0.496 AC: 1046 AN: 2110

Alfa AF: 0.525 Hom.: 48722

Bravo AF: 0.533

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9313730; hg19: chr5-175312710;