9-75376488-A-G

Variant names:

• chr9-75376488-A-G
• rs1409937

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 0.536 in 151,972 control chromosomes in the GnomAD database, including 22,707 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 (22707 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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: 0.536 AC: 81368 AN: 151854 Hom.: 22670 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.536 AC: 81453 AN: 151972 Hom.: 22707 Cov.: 31 AF XY: 0.534 AC XY: 39652 AN XY: 74284

African (AFR) AF: 0.704 AC: 29186 AN: 41442

American (AMR) AF: 0.444 AC: 6783 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2489 AN: 5150

South Asian (SAS) AF: 0.558 AC: 2695 AN: 4826

European-Finnish (FIN) AF: 0.450 AC: 4744 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32184 AN: 67954

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

Alfa AF: 0.494 Hom.: 60503

Bravo AF: 0.542

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.82
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1409937; hg19: chr9-77991404;