11-131333920-G-C

Variant names:

• chr11-131333920-G-C
• rs2511775
• ENST00000606885.1:n.147-16389G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606885.1(ENSG00000231698):​n.147-16389G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,768 control chromosomes in the GnomAD database, including 7,217 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 0.29 (7217 hom., cov: 31)
• Consequence: ENSG00000231698 ENST00000606885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 publications found

Genes affected

ENSG00000231698 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606885.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231698	ENST00000606885.1	TSL:1	n.147-16389G>C		intron	N/A
	ENSG00000231698	ENST00000834706.1		n.185-16389G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44236 AN: 151650 Hom.: 7211 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.292 AC: 44252 AN: 151768 Hom.: 7217 Cov.: 31 AF XY: 0.290 AC XY: 21471 AN XY: 74132

African (AFR) AF: 0.146 AC: 6060 AN: 41392

American (AMR) AF: 0.369 AC: 5625 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1248 AN: 5136

South Asian (SAS) AF: 0.198 AC: 953 AN: 4810

European-Finnish (FIN) AF: 0.331 AC: 3472 AN: 10482

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24841 AN: 67920

Other (OTH) AF: 0.293 AC: 616 AN: 2102

Alfa AF: 0.208 Hom.: 497

Bravo AF: 0.291

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.53
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2511775; hg19: chr11-131203815;