12-55607543-C-T

Variant names:

• chr12-55607543-C-T
• rs10747758
• ENST00000555138.2:n.85+21653G>A

Variant summary

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

The ENST00000555138.2(ENSG00000258763):​n.85+21653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,954 control chromosomes in the GnomAD database, including 20,841 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 0.50 (20841 hom., cov: 31)
• Consequence: ENSG00000258763 ENST00000555138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 5 publications found

Genes affected

ENSG00000258763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555138.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258763	ENST00000555138.2	TSL:2	n.85+21653G>A		intron	N/A
	ENSG00000258763	ENST00000556750.6	TSL:2	n.85+21653G>A		intron	N/A
	ENSG00000258763	ENST00000715996.1		n.586-22072G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75161 AN: 151836 Hom.: 20788 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.495 AC: 75268 AN: 151954 Hom.: 20841 Cov.: 31 AF XY: 0.498 AC XY: 36966 AN XY: 74266

African (AFR) AF: 0.750 AC: 31113 AN: 41472

American (AMR) AF: 0.426 AC: 6495 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1276 AN: 3462

East Asian (EAS) AF: 0.703 AC: 3628 AN: 5160

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4806

European-Finnish (FIN) AF: 0.396 AC: 4176 AN: 10546

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24926 AN: 67938

Other (OTH) AF: 0.467 AC: 982 AN: 2102

Alfa AF: 0.390 Hom.: 7635

Bravo AF: 0.508

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.60
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10747758; hg19: chr12-56001327;