ENST00000549203.2:n.143-48399C>T

Variant names:

• chr12-106556209-G-A
• rs4964469
• ENST00000549203.2:n.143-48399C>T

Variant summary

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

The ENST00000549203.2(ENSG00000257545):​n.143-48399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,858 control chromosomes in the GnomAD database, including 16,240 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 0.45 (16240 hom., cov: 32)
• Consequence: ENSG00000257545 ENST00000549203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 18 publications found

Genes affected

ENSG00000257545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549203.2. 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
	LOC100287944	NR_040246.1		n.143-48399C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257545	ENST00000549203.2	TSL:4	n.143-48399C>T		intron	N/A
	ENSG00000257545	ENST00000551505.4	TSL:4	n.230-56027C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68473 AN: 151740 Hom.: 16225 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.451 AC: 68521 AN: 151858 Hom.: 16240 Cov.: 32 AF XY: 0.451 AC XY: 33438 AN XY: 74172

African (AFR) AF: 0.593 AC: 24558 AN: 41406

American (AMR) AF: 0.350 AC: 5336 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1972 AN: 5162

South Asian (SAS) AF: 0.387 AC: 1859 AN: 4808

European-Finnish (FIN) AF: 0.516 AC: 5421 AN: 10514

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26574 AN: 67932

Other (OTH) AF: 0.404 AC: 852 AN: 2108

Alfa AF: 0.398 Hom.: 53964

Bravo AF: 0.443

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4964469; hg19: chr12-106949987;