rs11178531

Variant names:

• chr12-71014910-A-G
• rs11178531
• ENST00000552098.1:n.273+5788T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-71014910-A-G
• chr12-71014910-A-T

Variant summary

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

The ENST00000552098.1(ENSG00000257265):​n.273+5788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,924 control chromosomes in the GnomAD database, including 21,090 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 0.52 (21090 hom., cov: 32)
• Consequence: ENSG00000257265 ENST00000552098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 7 publications found

Genes affected

ENSG00000257265 (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 (AFR) allele frequency at 95% confidence interval = 0.565 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
ENSG00000257265	ENST00000552098.1	n.273+5788T>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78776 AN: 151804 Hom.: 21077 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.519 AC: 78827 AN: 151924 Hom.: 21090 Cov.: 32 AF XY: 0.515 AC XY: 38209 AN XY: 74244

African (AFR) AF: 0.571 AC: 23666 AN: 41426

American (AMR) AF: 0.388 AC: 5919 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1133 AN: 5160

South Asian (SAS) AF: 0.520 AC: 2498 AN: 4802

European-Finnish (FIN) AF: 0.578 AC: 6094 AN: 10544

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36603 AN: 67940

Other (OTH) AF: 0.470 AC: 994 AN: 2114

Alfa AF: 0.521 Hom.: 3917

Bravo AF: 0.501

Asia WGS AF: 0.343 AC: 1197 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	1.0
DANN	Benign	0.44
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs11178531; hg19: chr12-71408690;