rs11109504

chr12-78362131-G-Achr12-78362131-G-C

Variant summary

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

The ENST00000552230.5(ENSG00000258084):n.162+9451G>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 0.36 in 151,952 control chromosomes in the GnomAD database, including 10,285 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 0.36 (10285 hom., cov: 32)
• Consequence: ENST00000552230.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000552230.5	n.162+9451G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54622 AN: 151834 Hom.: 10285 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.360 AC: 54639 AN: 151952 Hom.: 10285 Cov.: 32 AF XY: 0.363 AC XY: 26998 AN XY: 74284

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.339

Alfa AF: 0.383 Hom.: 11045

Bravo AF: 0.340

Asia WGS AF: 0.312 AC: 1084 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.16
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11109504; hg19: chr12-78755911;