rs12229182

chr12-27110699-T-C

Variant summary

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

The ENST00000538920.1(ENSG00000256226):n.244-5441A>G 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 0.0732 in 152,194 control chromosomes in the GnomAD database, including 671 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 0.073 (671 hom., cov: 32)
• Consequence: ENST00000538920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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
	ENST00000538920.1	n.244-5441A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11131 AN: 152076 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0732 AC: 11144 AN: 152194 Hom.: 671 Cov.: 32 AF XY: 0.0769 AC XY: 5722 AN XY: 74412

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0880

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0701 Hom.: 445

Bravo AF: 0.0809

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12229182; hg19: chr12-27263632;