rs1109670

Positions:

• chr2-9109909-C-A
• chr2-9109909-C-G

Variant summary

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

The 2-9109909-C-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,240 control chromosomes in the GnomAD database, including 6,077 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 0.28 (6076 hom., cov: 34)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: ENST00000565044.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373414	XR_922767.2			downstream_gene_variant
LOC105373414	XR_007086201.1			downstream_gene_variant
LOC105373414	XR_922769.2			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000565044.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42180 AN: 152014 Hom.: 6062 Cov.: 34

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.227 AC: 25 AN: 110 Hom.: 1 Cov.: 0 AF XY: 0.289 AC XY: 22 AN XY: 76

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.278 AC: 42218 AN: 152130 Hom.: 6076 Cov.: 34 AF XY: 0.283 AC XY: 21074 AN XY: 74362

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.292

Alfa AF: 0.262 Hom.: 8470

Bravo AF: 0.281

Asia WGS AF: 0.419 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1109670; hg19: chr2-9250038;