rs12230172

Variant names:

• chr12-75848895-A-G
• rs12230172
• ENST00000552856.1:n.296-71365T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-75848895-A-G
• chr12-75848895-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552856.1(ENSG00000258077):​n.296-71365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,060 control chromosomes in the GnomAD database, including 18,179 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 0.48 (18179 hom., cov: 32)
• Consequence: ENSG00000258077 ENST00000552856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 6 publications found

Genes affected

ENSG00000258077 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258077	ENST00000552856.1	n.296-71365T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73198 AN: 151942 Hom.: 18191 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.481 AC: 73208 AN: 152060 Hom.: 18179 Cov.: 32 AF XY: 0.486 AC XY: 36113 AN XY: 74348

African (AFR) AF: 0.348 AC: 14418 AN: 41484

American (AMR) AF: 0.510 AC: 7792 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2298 AN: 5168

South Asian (SAS) AF: 0.517 AC: 2493 AN: 4818

European-Finnish (FIN) AF: 0.588 AC: 6216 AN: 10568

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36359 AN: 67954

Other (OTH) AF: 0.498 AC: 1048 AN: 2106

Alfa AF: 0.494 Hom.: 2482

Bravo AF: 0.467

Asia WGS AF: 0.472 AC: 1642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12230172; hg19: chr12-76242675;