rs3027009

Variant names:

• chr1-159204097-A-G
• rs3027009
• ENST00000609696.1:n.165-2476T>C

Variant summary

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

The ENST00000609696.1(CADM3-AS1):​n.165-2476T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,214 control chromosomes in the GnomAD database, including 330 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 0.058 (330 hom., cov: 31)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: CADM3-AS1 ENST00000609696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

CADM3-AS1 (HGNC:40812): (CADM3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM3-AS1	ENST00000609696.1	n.165-2476T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8793 AN: 152054 Hom.: 331 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0645

GnomAD4 exome AF: 0.100 AC: 4 AN: 40 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0577 AC: 8788 AN: 152174 Hom.: 330 Cov.: 31 AF XY: 0.0568 AC XY: 4225 AN XY: 74410

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0791 Hom.: 821

Bravo AF: 0.0573

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	7.4
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027009; hg19: chr1-159173887;