rs1909160

Positions:

• chr12-29993079-C-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 0.411 in 151,982 control chromosomes in the GnomAD database, including 13,728 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 0.41 (13728 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29993079C>T		intergenic_region
LOC105369715	XR_001749060.1	n.313+20673G>A		intron_variant
LOC105369715	XR_001749061.1	n.313+20673G>A		intron_variant
LOC105369715	XR_931474.1	n.313+20673G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62439 AN: 151864 Hom.: 13720 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.411 AC: 62459 AN: 151982 Hom.: 13728 Cov.: 32 AF XY: 0.409 AC XY: 30370 AN XY: 74270

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.447

Alfa AF: 0.432 Hom.: 3224

Bravo AF: 0.420

Asia WGS AF: 0.294 AC: 1025 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1909160; hg19: chr12-30146012;