ENST00000535764.1:n.153+58249C>G

Variant names:

• chr12-19833852-C-G
• rs12320955
• ENST00000535764.1:n.153+58249C>G

Variant summary

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

The ENST00000535764.1(ENSG00000255910):​n.153+58249C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,970 control chromosomes in the GnomAD database, including 4,643 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 0.24 (4643 hom., cov: 30)
• Consequence: ENSG00000255910 ENST00000535764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 2 publications found

Genes affected

ENSG00000255910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369682	XR_931409.3	n.709-1895G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255910	ENST00000535764.1	n.153+58249C>G		intron_variant	Intron 1 of 4	3
ENSG00000255910	ENST00000716354.1	n.256+58249C>G		intron_variant	Intron 1 of 10
ENSG00000255910	ENST00000716355.1	n.186+58249C>G		intron_variant	Intron 1 of 12

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36394 AN: 151852 Hom.: 4631 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36446 AN: 151970 Hom.: 4643 Cov.: 30 AF XY: 0.248 AC XY: 18396 AN XY: 74242

African (AFR) AF: 0.183 AC: 7576 AN: 41456

American (AMR) AF: 0.321 AC: 4898 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1327 AN: 5144

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4800

European-Finnish (FIN) AF: 0.365 AC: 3847 AN: 10536

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15823 AN: 67978

Other (OTH) AF: 0.238 AC: 503 AN: 2116

Alfa AF: 0.144 Hom.: 295

Bravo AF: 0.235

Asia WGS AF: 0.360 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12320955; hg19: chr12-19986786;