11-133542596-C-A

Position:

• chr11-133542596-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663344.1(ENSG00000287068):​n.295-6686C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,070 control chromosomes in the GnomAD database, including 4,989 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 0.23 (4989 hom., cov: 33)
• Consequence: ENST00000663344.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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
	ENST00000663344.1	n.295-6686C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34788 AN: 151952 Hom.: 4974 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.229 AC: 34847 AN: 152070 Hom.: 4989 Cov.: 33 AF XY: 0.235 AC XY: 17451 AN XY: 74328

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.193

Alfa AF: 0.140 Hom.: 2393

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11223500; hg19: chr11-133412491;