rs4111166

Positions:

• chr9-26524418-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.478 in 151,970 control chromosomes in the GnomAD database, including 17,686 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 0.48 (17686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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: 0.478 AC: 72546 AN: 151852 Hom.: 17658 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.478 AC: 72626 AN: 151970 Hom.: 17686 Cov.: 32 AF XY: 0.474 AC XY: 35227 AN XY: 74248

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.444

Alfa AF: 0.493 Hom.: 37986

Bravo AF: 0.467

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4111166; hg19: chr9-26524416; COSMIC: COSV69455209;