ENST00000549203.2:n.143-49107A>G

Variant names:

• chr12-106556917-T-C
• rs3891355
• ENST00000549203.2:n.143-49107A>G

Variant summary

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

The ENST00000549203.2(ENSG00000257545):​n.143-49107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,062 control chromosomes in the GnomAD database, including 1,312 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 0.12 (1312 hom., cov: 32)
• Consequence: ENSG00000257545 ENST00000549203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287944	NR_040246.1	n.143-49107A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257545	ENST00000549203.2	n.143-49107A>G		intron_variant	Intron 1 of 3	4
ENSG00000257545	ENST00000551505.4	n.230-56735A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18735 AN: 151944 Hom.: 1314 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.123 AC: 18727 AN: 152062 Hom.: 1312 Cov.: 32 AF XY: 0.122 AC XY: 9079 AN XY: 74300

African (AFR) AF: 0.0719 AC: 2982 AN: 41492

American (AMR) AF: 0.109 AC: 1666 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2004 AN: 10550

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10796 AN: 67972

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.141 Hom.: 4961

Bravo AF: 0.115

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.46
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: rs3891355; hg19: chr12-106950695;