rs1048903

chr10-79691789-A-Gchr10-79691789-A-T

Variant summary

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

The NR_120613.1(NUTM2B-AS1):n.1024T>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 0.255 in 150,068 control chromosomes in the GnomAD database, including 5,579 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 0.26 (5579 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2B-AS1 NR_120613.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

NUTM2B-AS1 (HGNC:51204): (NUTM2B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUTM2B-AS1	NR_120613.1	n.1024T>C		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTM2B-AS1	ENST00000671459.1	n.146-28555T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38288 AN: 149950 Hom.: 5566 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.287

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.255 AC: 38330 AN: 150068 Hom.: 5579 Cov.: 30 AF XY: 0.260 AC XY: 19036 AN XY: 73210

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.290

Alfa AF: 0.249 Hom.: 538

Bravo AF: 0.263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.39
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1048903; hg19: chr10-81451545;