ENST00000488805.6:n.750T>C

Variant names:

• chr10-79691789-A-G
• rs1048903
• ENST00000488805.6:n.750T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000488805.6(NUTM2B-AS1):​n.750T>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. There is a variant allele frequency bias in the population database for this variant (GnomAd4), which may indicate mosaicism or somatic mutations in the reference population data. 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 ENST00000488805.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488805.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B-AS1	NR_120613.1		n.1024T>C		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B-AS1	ENST00000488805.6	TSL:3	n.750T>C		non_coding_transcript_exon	Exon 6 of 6
	NUTM2B-AS1	ENST00000601369.7	TSL:2	n.946T>C		non_coding_transcript_exon	Exon 7 of 7
	NUTM2B-AS1	ENST00000662025.1		n.1168T>C		non_coding_transcript_exon	Exon 7 of 7

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.243 AC: 9927 AN: 40856

American (AMR) AF: 0.272 AC: 4091 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1316 AN: 3420

East Asian (EAS) AF: 0.684 AC: 3428 AN: 5010

South Asian (SAS) AF: 0.350 AC: 1637 AN: 4672

European-Finnish (FIN) AF: 0.208 AC: 2174 AN: 10436

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.221 AC: 14917 AN: 67352

Other (OTH) AF: 0.290 AC: 596 AN: 2058

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.249 Hom.: 538

Bravo AF: 0.263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1048903; hg19: chr10-81451545;