1-2569899-C-T

Position:

• chr1-2569899-C-T

Variant summary

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

The NR_121638.1(LOC100996583):​n.71+3294C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,820 control chromosomes in the GnomAD database, including 20,478 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 0.52 (20475 hom., cov: 31)
  • Exomes 𝑓: 0.33 (3 hom.)
• Consequence: LOC100996583 NR_121638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LOC100996583 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100996583	NR_121638.1	n.71+3294C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456687.3			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78327 AN: 151662 Hom.: 20464 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.497

GnomAD4 exome AF: 0.325 AC: 13 AN: 40 Hom.: 3 Cov.: 0 AF XY: 0.333 AC XY: 8 AN XY: 24

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.306

GnomAD4 genome AF: 0.516 AC: 78370 AN: 151780 Hom.: 20475 Cov.: 31 AF XY: 0.520 AC XY: 38559 AN XY: 74184

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.502

Alfa AF: 0.492 Hom.: 2948

Bravo AF: 0.513

Asia WGS AF: 0.659 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
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: rs10797432; hg19: chr1-2501338;