rs2871360

Positions:

• chr1-206503888-T-G

Variant summary

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

The XR_007066830.1(LOC124904493):​n.1775A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,050 control chromosomes in the GnomAD database, including 12,690 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 0.39 (12689 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: LOC124904493 XR_007066830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

LOC124904493 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904493	XR_007066830.1	n.1775A>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59697 AN: 151926 Hom.: 12689 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.393 AC: 59731 AN: 152044 Hom.: 12689 Cov.: 32 AF XY: 0.391 AC XY: 29028 AN XY: 74312

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.395

Alfa AF: 0.423 Hom.: 2350

Bravo AF: 0.384

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.28
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2871360; hg19: chr1-206677221;