rs12815666

Positions:

• chr12-112977949-C-T

Variant summary

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

The ENST00000552784.1(ENSG00000257452):​n.353+39450G>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 0.101 in 152,154 control chromosomes in the GnomAD database, including 960 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 0.10 (960 hom., cov: 31)
• Consequence: ENST00000552784.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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
	ENST00000552784.1	n.353+39450G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15352 AN: 152036 Hom.: 960 Cov.: 31

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.101 AC: 15344 AN: 152154 Hom.: 960 Cov.: 31 AF XY: 0.0987 AC XY: 7340 AN XY: 74388

Gnomad4 AFR AF: 0.0407

Gnomad4 AMR AF: 0.0886

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0900

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.110

Alfa AF: 0.108 Hom.: 135

Bravo AF: 0.0939

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12815666; hg19: chr12-113415754;