9-97895438-A-T

Variant names:

• chr9-97895438-A-T
• rs7036589

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.725 in 151,898 control chromosomes in the GnomAD database, including 41,329 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 0.73 (41329 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.725 AC: 110088 AN: 151780 Hom.: 41277 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.725 AC: 110190 AN: 151898 Hom.: 41329 Cov.: 30 AF XY: 0.728 AC XY: 53996 AN XY: 74220

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.707

Alfa AF: 0.683 Hom.: 4539

Bravo AF: 0.739

Asia WGS AF: 0.781 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7036589; hg19: chr9-100657720;