rs2293877

Variant names:

• chr14-70469158-A-G
• rs2293877
• ENST00000556964.1:n.2757T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-70469158-A-G
• chr14-70469158-A-T

Variant summary

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

The ENST00000556964.1(ADAM20P1):​n.2757T>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 0.207 in 152,198 control chromosomes in the GnomAD database, including 4,917 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 0.21 (4917 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADAM20P1 ENST00000556964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66
• Publications: 6 publications found

Genes affected

ADAM20P1 (HGNC:):

ADAM20P1 (HGNC:20102): (ADAM metallopeptidase domain 20 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556964.1. 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
	ADAM20P1	NR_037933.1		n.2757T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM20P1	ENST00000556964.1	TSL:1	n.2757T>C		non_coding_transcript_exon	Exon 2 of 2
	ADAM20P1	ENST00000320746.6	TSL:6	n.2049T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000257759	ENST00000556646.1	TSL:4	n.184-15649T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31537 AN: 152080 Hom.: 4909 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.215

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) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.207 AC: 31578 AN: 152198 Hom.: 4917 Cov.: 32 AF XY: 0.203 AC XY: 15120 AN XY: 74424

African (AFR) AF: 0.382 AC: 15851 AN: 41478

American (AMR) AF: 0.157 AC: 2398 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3462

East Asian (EAS) AF: 0.604 AC: 3125 AN: 5174

South Asian (SAS) AF: 0.158 AC: 761 AN: 4822

European-Finnish (FIN) AF: 0.0761 AC: 808 AN: 10620

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7290 AN: 68016

Other (OTH) AF: 0.220 AC: 466 AN: 2114

Alfa AF: 0.146 Hom.: 7165

Bravo AF: 0.225

Asia WGS AF: 0.389 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	16
DANN	Benign	0.61
PhyloP100		2.7

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: rs2293877;

hg19: chr14-70935875;