chr1-150579854-G-T

Position:

• chr1-150579854-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001738230.3(LOC107985203):​n.25G>T 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 0.477 in 291,584 control chromosomes in the GnomAD database, including 36,629 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 0.43 (15887 hom., cov: 30)
  • Exomes 𝑓: 0.53 (20742 hom.)
• Consequence: LOC107985203 XR_001738230.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

LOC107985203 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985203	XR_001738230.3	n.25G>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65176 AN: 151486 Hom.: 15893 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.528 AC: 73867 AN: 139982 Hom.: 20742 AF XY: 0.527 AC XY: 37068 AN XY: 70332

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.413

Gnomad4 ASJ exome AF: 0.412

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.644

Gnomad4 NFE exome AF: 0.574

Gnomad4 OTH exome AF: 0.504

GnomAD4 genome AF: 0.430 AC: 65165 AN: 151602 Hom.: 15887 Cov.: 30 AF XY: 0.431 AC XY: 31916 AN XY: 74026

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.451

Alfa AF: 0.484 Hom.: 3203

Bravo AF: 0.404

Asia WGS AF: 0.395 AC: 1369 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	15
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738484; hg19: chr1-150552330;