rs11178531

Positions:

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

Variant summary

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

The ENST00000552098.1(ENSG00000257265):​n.273+5788T>C 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 0.519 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: ENST00000552098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552098.1	n.273+5788T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.470

Alfa AF: 0.520 Hom.: 3800

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11178531; hg19: chr12-71408690;