rs1596725

Positions:

• chr12-65028591-A-C
• chr12-65028591-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000198671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000198671	ENST00000360528.3	n.1035+8350A>C		intron_variant		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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.405

Alfa AF: 0.348 Hom.: 4244

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1596725; hg19: chr12-65422371;