11-4145756-C-T

Variant names:

• chr11-4145756-C-T
• rs10500594

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 0.88 in 152,062 control chromosomes in the GnomAD database, including 59,138 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 (59138 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 (SAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133720 AN: 151944 Hom.: 59135 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.880 AC: 133762 AN: 152062 Hom.: 59138 Cov.: 30 AF XY: 0.875 AC XY: 65056 AN XY: 74320

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.872

Alfa AF: 0.910 Hom.: 10510

Bravo AF: 0.870

Asia WGS AF: 0.788 AC: 2741 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	8.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500594; hg19: chr11-4166986;