10-79763599-C-A

Variant names:

• chr10-79763599-C-A
• rs186749160
• ENST00000610681.1:n.3352G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000610681.1(NUTM2B-AS1):​n.3352G>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 0.00903 in 151,822 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0090 (31 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2B-AS1 ENST00000610681.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.241
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 10-79763599-C-A is Benign according to our data. Variant chr10-79763599-C-A is described in ClinVar as Benign. ClinVar VariationId is 3771723.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 1371 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610681.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B-AS1	NR_120611.1		n.3428G>T		non_coding_transcript_exon	Exon 6 of 6
	NUTM2B-AS1	NR_120613.1		n.756+2672G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B-AS1	ENST00000610681.1	TSL:1	n.3352G>T		non_coding_transcript_exon	Exon 2 of 2
	NUTM2B-AS1	ENST00000665716.2		n.3323G>T		non_coding_transcript_exon	Exon 6 of 6
	NUTM2B-AS1	ENST00000477192.6	TSL:5	n.862+2672G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00904 AC: 1371 AN: 151708 Hom.: 31 Cov.: 31

Gnomad AFR AF: 0.00276

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00901

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00272

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.00912

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.00903 AC: 1371 AN: 151822 Hom.: 31 Cov.: 31 AF XY: 0.00815 AC XY: 605 AN XY: 74208

African (AFR) AF: 0.00275 AC: 114 AN: 41426

American (AMR) AF: 0.00900 AC: 137 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 4 AN: 3460

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5148

South Asian (SAS) AF: 0.00272 AC: 13 AN: 4784

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10550

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0141 AC: 956 AN: 67928

Other (OTH) AF: 0.00902 AC: 19 AN: 2106

Alfa AF: 0.0114 Hom.: 4

Bravo AF: 0.00846

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.66
PhyloP100		0.24
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs186749160; hg19: chr10-81523355;