rs9297759

Positions:

• chr8-127506926-A-C
• chr8-127506926-A-T

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 0.883 in 152,086 control chromosomes in the GnomAD database, including 59,330 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 0.88 (59330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.906 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: 0.883 AC: 134147 AN: 151968 Hom.: 59287 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.883 AC: 134247 AN: 152086 Hom.: 59330 Cov.: 32 AF XY: 0.881 AC XY: 65512 AN XY: 74336

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.898

Alfa AF: 0.884 Hom.: 7796

Bravo AF: 0.885

Asia WGS AF: 0.820 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297759; hg19: chr8-128519171;