12-48015514-C-T

Variant names:

• chr12-48015514-C-T
• rs11168354
• ENST00000546738.1:n.392+1324C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000546738.1(ENSG00000257985):​n.392+1324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,198 control chromosomes in the GnomAD database, including 5,321 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 0.22 (5321 hom., cov: 32)
• Consequence: ENSG00000257985 ENST00000546738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805
• Publications: 3 publications found

Genes affected

ENSG00000257985 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546738.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257985	ENST00000546738.1	TSL:2	n.392+1324C>T		intron	N/A
	ENSG00000257985	ENST00000823329.1		n.362+1324C>T		intron	N/A
	ENSG00000257985	ENST00000823330.1		n.257+1324C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32742 AN: 152080 Hom.: 5319 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.215 AC: 32770 AN: 152198 Hom.: 5321 Cov.: 32 AF XY: 0.212 AC XY: 15793 AN XY: 74414

African (AFR) AF: 0.456 AC: 18937 AN: 41502

American (AMR) AF: 0.115 AC: 1762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.165 AC: 856 AN: 5184

South Asian (SAS) AF: 0.141 AC: 681 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1554 AN: 10598

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8043 AN: 68014

Other (OTH) AF: 0.180 AC: 380 AN: 2116

Alfa AF: 0.188 Hom.: 545

Bravo AF: 0.225

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.41
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs11168354; hg19: chr12-48409297;