rs4590917

Variant names:

• chr12-93033819-T-C
• rs4590917
• ENST00000549930.1:n.99-29221A>G

Variant summary

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

The ENST00000550324.7(ENSG00000257252):​n.169-29221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,134 control chromosomes in the GnomAD database, including 1,884 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 0.15 (1884 hom., cov: 32)
• Consequence: ENSG00000257252 ENST00000550324.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 3 publications found

Genes affected

ENSG00000257252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550324.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC643339	NR_040096.1		n.428-29221A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257252	ENST00000549930.1	TSL:5	n.99-29221A>G		intron	N/A
	ENSG00000257252	ENST00000550324.7	TSL:3	n.169-29221A>G		intron	N/A
	ENSG00000257252	ENST00000754393.1		n.767-29221A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22875 AN: 152016 Hom.: 1879 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.151 AC: 22915 AN: 152134 Hom.: 1884 Cov.: 32 AF XY: 0.151 AC XY: 11240 AN XY: 74376

African (AFR) AF: 0.213 AC: 8827 AN: 41476

American (AMR) AF: 0.0948 AC: 1450 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3472

East Asian (EAS) AF: 0.155 AC: 801 AN: 5184

South Asian (SAS) AF: 0.300 AC: 1442 AN: 4812

European-Finnish (FIN) AF: 0.0979 AC: 1039 AN: 10610

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8349 AN: 67972

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.132 Hom.: 1767

Bravo AF: 0.149

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4590917; hg19: chr12-93427595;