chr1-217920809-G-A

Position:

• chr1-217920809-G-A

Variant summary

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

The XR_001738466.2(LOC105372922):​n.857+741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,040 control chromosomes in the GnomAD database, including 37,794 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 0.70 (37793 hom., cov: 31)
  • Exomes 𝑓: 0.43 (1 hom.)
• Consequence: LOC105372922 XR_001738466.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

Genes affected

LOC105372922 (HGNC:):

LINC00210 (HGNC:37458): (long intergenic non-protein coding RNA 210)

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 (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372922	XR_001738466.2	n.857+741C>T		intron_variant
LINC00210	NR_048550.1	n.*5G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00210	ENST00000431637.2	n.*5G>A		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106483 AN: 151910 Hom.: 37760 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.684

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.429 AC XY: 6 AN XY: 14

Gnomad4 NFE exome AF: 0.429

GnomAD4 genome AF: 0.701 AC: 106561 AN: 152026 Hom.: 37793 Cov.: 31 AF XY: 0.695 AC XY: 51662 AN XY: 74298

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.677

Alfa AF: 0.703 Hom.: 77396

Bravo AF: 0.705

Asia WGS AF: 0.523 AC: 1819 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	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6604568; hg19: chr1-218094151;