2-173281723-G-C

Variant names:

• chr2-173281723-G-C
• rs711794
• ENST00000423106.2:n.314C>G

Variant summary

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

The ENST00000423106.2(MAP3K20-AS1):​n.314C>G 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 0.107 in 152,296 control chromosomes in the GnomAD database, including 1,139 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 0.11 (1139 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: MAP3K20-AS1 ENST00000423106.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 2 publications found

Genes affected

MAP3K20-AS1 (HGNC:27935): (MAP3K20 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423106.2. 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
	MAP3K20-AS1	NR_033882.1		n.314C>G		non_coding_transcript_exon	Exon 1 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K20-AS1	ENST00000423106.2	TSL:1	n.314C>G		non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16220 AN: 152024 Hom.: 1138 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.0766

GnomAD4 exome AF: 0.104 AC: 16 AN: 154 Hom.: 0 Cov.: 0 AF XY: 0.0794 AC XY: 10 AN XY: 126

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

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: 0.104 AC: 14 AN: 134

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.107 AC: 16243 AN: 152142 Hom.: 1139 Cov.: 32 AF XY: 0.106 AC XY: 7877 AN XY: 74370

African (AFR) AF: 0.195 AC: 8085 AN: 41462

American (AMR) AF: 0.0559 AC: 855 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1104 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0800 AC: 5440 AN: 68008

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0524 Hom.: 53

Bravo AF: 0.105

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.68
PhyloP100		-0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs711794;

hg19: chr2-174146451;