chr11-32057675-C-T

Variant names:

• chr11-32057675-C-T
• rs12420599
• ENST00000532942.5:c.102-39469C>T

Variant summary

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

The ENST00000532942.5(ENSG00000285283):​c.102-39469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,128 control chromosomes in the GnomAD database, including 3,260 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 0.19 (3260 hom., cov: 32)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 5 publications found

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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
ENSG00000285283	ENST00000532942.5	c.102-39469C>T		intron_variant	Intron 1 of 5	2		ENSP00000436422.1
ENSG00000285283	ENST00000530348.5	c.-244-39469C>T		intron_variant	Intron 1 of 3	4		ENSP00000436482.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28287 AN: 152010 Hom.: 3257 Cov.: 32

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.186 AC: 28294 AN: 152128 Hom.: 3260 Cov.: 32 AF XY: 0.188 AC XY: 13942 AN XY: 74352

African (AFR) AF: 0.0513 AC: 2131 AN: 41514

American (AMR) AF: 0.259 AC: 3964 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 588 AN: 3464

East Asian (EAS) AF: 0.419 AC: 2162 AN: 5166

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2080 AN: 10576

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15328 AN: 67986

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.202 Hom.: 7204

Bravo AF: 0.188

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12420599; hg19: chr11-32079221;