rs1422876

Positions:

• chr5-159334291-C-T

Variant summary

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

The NR_037889.1(LOC285626):​n.745+1288C>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 0.546 in 151,886 control chromosomes in the GnomAD database, including 23,124 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 0.55 (23124 hom., cov: 31)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.745+1288C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000515337.1	n.745+1288C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.324+1288C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82836 AN: 151770 Hom.: 23090 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.546 AC: 82916 AN: 151886 Hom.: 23124 Cov.: 31 AF XY: 0.546 AC XY: 40500 AN XY: 74214

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.525

Alfa AF: 0.526 Hom.: 3122

Bravo AF: 0.542

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1422876; hg19: chr5-158761299;