rs1121541

Positions:

• chr9-12667049-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 0.428 in 151,936 control chromosomes in the GnomAD database, including 18,339 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 0.43 (18339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

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 (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.428 AC: 64964 AN: 151818 Hom.: 18343 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.428 AC: 64956 AN: 151936 Hom.: 18339 Cov.: 31 AF XY: 0.422 AC XY: 31369 AN XY: 74260

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.431

Alfa AF: 0.520 Hom.: 5023

Bravo AF: 0.387

Asia WGS AF: 0.138 AC: 482 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	0.46
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1121541; hg19: chr9-12667049;