9-5188078-A-G

Variant names:

• chr9-5188078-A-G
• rs10758677

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 0.588 in 152,146 control chromosomes in the GnomAD database, including 28,149 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 0.59 (28149 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89384 AN: 152028 Hom.: 28102 Cov.: 33

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.588 AC: 89487 AN: 152146 Hom.: 28149 Cov.: 33 AF XY: 0.586 AC XY: 43589 AN XY: 74374

African (AFR) AF: 0.823 AC: 34191 AN: 41542

American (AMR) AF: 0.561 AC: 8576 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1911 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1971 AN: 5184

South Asian (SAS) AF: 0.499 AC: 2400 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5765 AN: 10544

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32755 AN: 67976

Other (OTH) AF: 0.582 AC: 1232 AN: 2116

Alfa AF: 0.511 Hom.: 33320

Bravo AF: 0.598

Asia WGS AF: 0.497 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10758677; hg19: chr9-5188078;