rs953509

chr9-79755612-T-Achr9-79755612-T-Cchr9-79755612-T-G

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 0.681 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.663

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953509; hg19: chr9-82370527;