rs4576883

Positions:

• chr12-119251654-A-G

Variant summary

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

The ENST00000536009.1(ENSG00000256311):​n.69+7295T>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 0.143 in 152,220 control chromosomes in the GnomAD database, including 1,668 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 0.14 (1668 hom., cov: 33)
• Consequence: ENST00000536009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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
	ENST00000536009.1	n.69+7295T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21669 AN: 152100 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.143 AC: 21696 AN: 152220 Hom.: 1668 Cov.: 33 AF XY: 0.141 AC XY: 10507 AN XY: 74416

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.147

Alfa AF: 0.128 Hom.: 1260

Bravo AF: 0.140

Asia WGS AF: 0.194 AC: 676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4576883; hg19: chr12-119689459;