rs2584316

Positions:

• chr1-222037987-A-G

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 0.362 in 152,000 control chromosomes in the GnomAD database, including 10,310 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 0.36 (10310 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.222037987A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000658927.1	n.382-4316T>C		intron_variant
LINC01705	ENST00000668844.1	n.354+20427T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55059 AN: 151882 Hom.: 10314 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.362 AC: 55065 AN: 152000 Hom.: 10310 Cov.: 32 AF XY: 0.367 AC XY: 27261 AN XY: 74302

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.374

Alfa AF: 0.382 Hom.: 6549

Bravo AF: 0.349

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2584316; hg19: chr1-222211329; COSMIC: COSV71538787;