chr1-159204097-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609696.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM3-AS1	ENST00000609696.1	TSL:5	n.165-2476T>C		intron	N/A

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

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) AF: 0.167 AC: 3 AN: 18

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0500 AC: 1 AN: 20

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

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

African (AFR) AF: 0.0166 AC: 689 AN: 41510

American (AMR) AF: 0.0701 AC: 1071 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4820

European-Finnish (FIN) AF: 0.0653 AC: 692 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0854 AC: 5804 AN: 67988

Other (OTH) AF: 0.0629 AC: 133 AN: 2116

Alfa AF: 0.0752 Hom.: 1700

Bravo AF: 0.0573

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	7.4
DANN	Benign	0.87
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3027009; hg19: chr1-159173887;