rs12576211

Positions:

• chr11-125116097-G-A

Variant summary

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

The ENST00000534728.1(ENSG00000293069):​n.1785+1152G>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 0.268 in 152,020 control chromosomes in the GnomAD database, including 6,518 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 0.27 (6518 hom., cov: 32)
• Consequence: ENST00000534728.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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
	ENST00000534728.1	n.1785+1152G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40618 AN: 151902 Hom.: 6503 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.268 AC: 40668 AN: 152020 Hom.: 6518 Cov.: 32 AF XY: 0.261 AC XY: 19395 AN XY: 74314

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.244

Alfa AF: 0.226 Hom.: 2909

Bravo AF: 0.277

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0070
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12576211; hg19: chr11-124985993;