2-173281723-G-C

Position:

• chr2-173281723-G-C

Variant summary

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

The NR_033882.1(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 NR_033882.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K20-AS1	NR_033882.1	n.314C>G		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K20-AS1	ENST00000423106.2	n.314C>G		non_coding_transcript_exon_variant	1/8	1

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

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.167

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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0800

Gnomad4 OTH AF: 0.0758

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs711794; hg19: chr2-174146451;