rs2293877

chr14-70469158-A-Gchr14-70469158-A-T

Variant summary

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

The NR_037933.1(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 NR_037933.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAM20P1	NR_037933.1	n.2757T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM20P1	ENST00000320746.6	n.2049T>C		non_coding_transcript_exon_variant	1/1
ADAM20P1	ENST00000556964.1	n.2757T>C		non_coding_transcript_exon_variant	2/2	1
	ENST00000556646.1	n.184-15649T>C		intron_variant, non_coding_transcript_variant		4
ADAM20P1	ENST00000649019.1	n.342-8544T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.220

Alfa AF: 0.130 Hom.: 3431

Bravo AF: 0.225

Asia WGS AF: 0.389 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	16
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293877; hg19: chr14-70935875;