11-4145756-C-T

Variant names:

• chr11-4145756-C-T
• rs10500594

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.812 AC: 33662 AN: 41454

American (AMR) AF: 0.853 AC: 13035 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3178 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3861 AN: 5130

South Asian (SAS) AF: 0.933 AC: 4500 AN: 4824

European-Finnish (FIN) AF: 0.886 AC: 9380 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63320 AN: 67996

Other (OTH) AF: 0.872 AC: 1841 AN: 2112

Alfa AF: 0.898 Hom.: 20702

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
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs10500594; hg19: chr11-4166986;