rs10488710

Variant names:

• chr11-115336457-C-G
• rs10488710
• NM_001301043.2:c.125-96037G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-115336457-C-G
• chr11-115336457-C-T

Variant summary

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

The NM_001301043.2(CADM1):​c.125-96037G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,020 control chromosomes in the GnomAD database, including 30,287 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 0.63 (30287 hom., cov: 32)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 18 publications found

Genes affected

CADM1 (HGNC:5951): (cell adhesion molecule 1) Enables signaling receptor binding activity. Involved in several processes, including cell recognition; positive regulation of cytokine production; and susceptibility to natural killer cell mediated cytotoxicity. Located in plasma membrane. Implicated in breast carcinoma and prostate cancer. Biomarker of cervix uteri carcinoma in situ. [provided by Alliance of Genome Resources, Apr 2022]

CADM1 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000256972 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001301043.2. 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
	CADM1	NM_001301043.2	MANE Select	c.125-96037G>C		intron	N/A	NP_001287972.1	Q9BY67-3
	CADM1	NM_001301044.2		c.125-96037G>C		intron	N/A	NP_001287973.1	X5DQR8
	CADM1	NM_001301045.2		c.125-96037G>C		intron	N/A	NP_001287974.1	X5DQS5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM1	ENST00000331581.11	TSL:1 MANE Select	c.125-96037G>C		intron	N/A	ENSP00000329797.6	Q9BY67-3
	CADM1	ENST00000537058.5	TSL:1	c.125-96037G>C		intron	N/A	ENSP00000439817.1	Q9BY67-4
	CADM1	ENST00000536727.5	TSL:1	c.125-96037G>C		intron	N/A	ENSP00000440322.1	X5DQS5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95539 AN: 151902 Hom.: 30253 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.620

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.629 AC: 95634 AN: 152020 Hom.: 30287 Cov.: 32 AF XY: 0.631 AC XY: 46876 AN XY: 74304

African (AFR) AF: 0.602 AC: 24931 AN: 41446

American (AMR) AF: 0.633 AC: 9656 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1778 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3179 AN: 5174

South Asian (SAS) AF: 0.690 AC: 3333 AN: 4828

European-Finnish (FIN) AF: 0.672 AC: 7116 AN: 10582

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43728 AN: 67948

Other (OTH) AF: 0.623 AC: 1319 AN: 2116

Alfa AF: 0.627 Hom.: 3550

Bravo AF: 0.621

Asia WGS AF: 0.629 AC: 2187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.43
PhyloP100		-0.87
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: rs10488710; hg19: chr11-115207176;