ENST00000360528.3:n.1035+8350A>C

Variant names:

• chr12-65028591-A-C
• rs1596725
• ENST00000360528.3:n.1035+8350A>C

Variant summary

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

The ENST00000360528.3(ENSG00000198671):​n.1035+8350A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 142,144 control chromosomes in the GnomAD database, including 8,712 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 0.35 (8712 hom., cov: 30)
• Consequence: ENSG00000198671 ENST00000360528.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 publications found

Genes affected

ENSG00000198671 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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
ENSG00000198671	ENST00000360528.3	n.1035+8350A>C		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.349 AC: 49619 AN: 142036 Hom.: 8704 Cov.: 30

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.349 AC: 49643 AN: 142144 Hom.: 8712 Cov.: 30 AF XY: 0.351 AC XY: 24183 AN XY: 68820

African (AFR) AF: 0.246 AC: 9016 AN: 36600

American (AMR) AF: 0.315 AC: 4333 AN: 13764

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1553 AN: 3416

East Asian (EAS) AF: 0.439 AC: 2183 AN: 4978

South Asian (SAS) AF: 0.409 AC: 1800 AN: 4406

European-Finnish (FIN) AF: 0.351 AC: 3346 AN: 9534

Middle Eastern (MID) AF: 0.497 AC: 142 AN: 286

European-Non Finnish (NFE) AF: 0.393 AC: 26066 AN: 66314

Other (OTH) AF: 0.405 AC: 789 AN: 1948

Alfa AF: 0.352 Hom.: 4827

Bravo AF: 0.319

Asia WGS AF: 0.410 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.66
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1596725; hg19: chr12-65422371;