ENST00000800118.1:n.405C>T

Variant names:

• chr12-65537114-G-A
• rs2245210
• ENST00000800118.1:n.405C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000800118.1(ENSG00000304153):​n.405C>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 0.173 in 152,140 control chromosomes in the GnomAD database, including 2,706 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 0.17 (2706 hom., cov: 33)
• Consequence: ENSG00000304153 ENST00000800118.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 4 publications found

Genes affected

ENSG00000304153 (HGNC:):

MSRB3-AS1 (HGNC:53386): (MSRB3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800118.1. 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
	MSRB3-AS1	NR_120431.1		n.392+32877C>T		intron	N/A
	MSRB3-AS1	NR_120432.1		n.565+32877C>T		intron	N/A
	MSRB3-AS1	NR_120433.1		n.569+1570C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304153	ENST00000800118.1		n.405C>T		non_coding_transcript_exon	Exon 3 of 3
	MSRB3-AS1	ENST00000535315.5	TSL:3	n.350+32877C>T		intron	N/A
	MSRB3-AS1	ENST00000537250.5	TSL:3	n.218+32877C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26246 AN: 152022 Hom.: 2701 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 26258 AN: 152140 Hom.: 2706 Cov.: 33 AF XY: 0.171 AC XY: 12734 AN XY: 74376

African (AFR) AF: 0.0749 AC: 3109 AN: 41526

American (AMR) AF: 0.274 AC: 4192 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1367 AN: 5144

South Asian (SAS) AF: 0.0963 AC: 465 AN: 4828

European-Finnish (FIN) AF: 0.137 AC: 1451 AN: 10582

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14385 AN: 67994

Other (OTH) AF: 0.171 AC: 361 AN: 2116

Alfa AF: 0.204 Hom.: 4676

Bravo AF: 0.181

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.67
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs2245210; hg19: chr12-65930894;