12-17509301-A-T

Position:

• chr12-17509301-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.479 in 151,892 control chromosomes in the GnomAD database, including 17,871 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 (17871 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17509301A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256389	ENST00000669683.1	n.965+4249A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72730 AN: 151774 Hom.: 17836 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.479 AC: 72820 AN: 151892 Hom.: 17871 Cov.: 32 AF XY: 0.484 AC XY: 35956 AN XY: 74248

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.480

Alfa AF: 0.341 Hom.: 993

Bravo AF: 0.493

Asia WGS AF: 0.665 AC: 2312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1706631; hg19: chr12-17662235;