12-48015514-C-T

Position:

• chr12-48015514-C-T

Variant summary

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

The ENST00000546738.1(ENSG00000257985):​n.392+1324C>T 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 0.215 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: ENST00000546738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

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 (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369750	XR_001749115.3	n.88+1324C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000546738.1	n.392+1324C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.180

Alfa AF: 0.178 Hom.: 471

Bravo AF: 0.225

Asia WGS AF: 0.172 AC: 598 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	6.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11168354; hg19: chr12-48409297;