12-55607402-G-A

Variant names:

• chr12-55607402-G-A
• rs4759173
• ENST00000555138.2:n.85+21794C>T

Variant summary

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

The ENST00000555138.2(ENSG00000258763):​n.85+21794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,998 control chromosomes in the GnomAD database, including 12,823 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 0.41 (12823 hom., cov: 32)
• Consequence: ENSG00000258763 ENST00000555138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258763	ENST00000555138.2	TSL:2	n.85+21794C>T		intron	N/A
	ENSG00000258763	ENST00000556750.6	TSL:2	n.85+21794C>T		intron	N/A
	ENSG00000258763	ENST00000715996.1		n.586-21931C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61805 AN: 151880 Hom.: 12804 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.407 AC: 61867 AN: 151998 Hom.: 12823 Cov.: 32 AF XY: 0.411 AC XY: 30566 AN XY: 74298

African (AFR) AF: 0.476 AC: 19717 AN: 41454

American (AMR) AF: 0.383 AC: 5852 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2630 AN: 5174

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4160 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24816 AN: 67946

Other (OTH) AF: 0.403 AC: 851 AN: 2110

Alfa AF: 0.316 Hom.: 1764

Bravo AF: 0.406

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4759173; hg19: chr12-56001186;