chr12-21129636-T-C

Variant names:

• chr12-21129636-T-C
• rs17328763
• ENST00000593147.5:n.*115-1487T>C

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*115-1487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,046 control chromosomes in the GnomAD database, including 1,775 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 0.13 (1775 hom., cov: 32)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 8 publications found

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593147.5. 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
	ENSG00000257062	ENST00000593147.5	TSL:5	n.*115-1487T>C		intron	N/A	ENSP00000467209.1
	ENSG00000257062	ENST00000543498.5	TSL:4	n.279-11878T>C		intron	N/A	ENSP00000454306.1
	ENSG00000257062	ENST00000585342.5	TSL:4	n.*101-1487T>C		intron	N/A	ENSP00000467594.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19779 AN: 151928 Hom.: 1776 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.130 AC: 19773 AN: 152046 Hom.: 1775 Cov.: 32 AF XY: 0.124 AC XY: 9225 AN XY: 74344

African (AFR) AF: 0.0360 AC: 1494 AN: 41506

American (AMR) AF: 0.139 AC: 2113 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3464

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5156

South Asian (SAS) AF: 0.0680 AC: 328 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10600

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13051 AN: 67950

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.177 Hom.: 3489

Bravo AF: 0.131

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.61
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs17328763; hg19: chr12-21282570;