chr9-79755612-T-A

Variant names:

• chr9-79755612-T-A
• rs953509

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 0.681 in 152,126 control chromosomes in the GnomAD database, including 35,882 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 0.68 (35882 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.681 AC: 103502 AN: 152008 Hom.: 35877 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.681 AC: 103537 AN: 152126 Hom.: 35882 Cov.: 33 AF XY: 0.685 AC XY: 50943 AN XY: 74388

African (AFR) AF: 0.555 AC: 23008 AN: 41470

American (AMR) AF: 0.645 AC: 9868 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2327 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3938 AN: 5170

South Asian (SAS) AF: 0.725 AC: 3495 AN: 4824

European-Finnish (FIN) AF: 0.827 AC: 8767 AN: 10602

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49858 AN: 67980

Other (OTH) AF: 0.663 AC: 1402 AN: 2114

Alfa AF: 0.699 Hom.: 4662

Bravo AF: 0.662

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.62
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs953509; hg19: chr9-82370527;