rs1335256

Positions:

• chr9-118564751-C-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 0.689 in 151,990 control chromosomes in the GnomAD database, including 36,439 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 0.69 (36439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104708 AN: 151872 Hom.: 36414 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.689 AC: 104784 AN: 151990 Hom.: 36439 Cov.: 32 AF XY: 0.689 AC XY: 51170 AN XY: 74290

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.715

Alfa AF: 0.691 Hom.: 6181

Bravo AF: 0.681

Asia WGS AF: 0.598 AC: 2078 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335256; hg19: chr9-121327029;