rs10891802

Variant names:

• chr11-115173168-C-A
• rs10891802
• NM_001301043.2:c.*3306G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-115173168-C-A
• chr11-115173168-C-G
• chr11-115173168-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.*3306G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,878 control chromosomes in the GnomAD database, including 16,007 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 0.44 (15996 hom., cov: 31)
  • Exomes 𝑓: 0.51 (11 hom.)
• Consequence: CADM1 NM_001301043.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 9 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM1	NM_001301043.2	MANE Select	c.*3306G>T		3_prime_UTR	Exon 12 of 12	NP_001287972.1
	CADM1	NM_001301044.2		c.*3306G>T		3_prime_UTR	Exon 11 of 11	NP_001287973.1
	CADM1	NM_001301045.2		c.*3306G>T		3_prime_UTR	Exon 11 of 11	NP_001287974.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM1	ENST00000331581.11	TSL:1 MANE Select	c.*3306G>T		3_prime_UTR	Exon 12 of 12	ENSP00000329797.6
	CADM1	ENST00000452722.7	TSL:1	c.*3306G>T		3_prime_UTR	Exon 10 of 10	ENSP00000395359.2
	CADM1	ENST00000537140.5	TSL:1	n.1256-3542G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67021 AN: 151684 Hom.: 15998 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.513 AC: 40 AN: 78 Hom.: 11 Cov.: 0 AF XY: 0.516 AC XY: 33 AN XY: 64

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 8 AN: 12

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.565 AC: 26 AN: 46

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.442 AC: 67031 AN: 151800 Hom.: 15996 Cov.: 31 AF XY: 0.445 AC XY: 33002 AN XY: 74174

African (AFR) AF: 0.266 AC: 11017 AN: 41368

American (AMR) AF: 0.406 AC: 6211 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1753 AN: 3464

East Asian (EAS) AF: 0.488 AC: 2514 AN: 5150

South Asian (SAS) AF: 0.514 AC: 2468 AN: 4798

European-Finnish (FIN) AF: 0.531 AC: 5577 AN: 10500

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35877 AN: 67924

Other (OTH) AF: 0.458 AC: 966 AN: 2110

Alfa AF: 0.492 Hom.: 45512

Bravo AF: 0.424

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10891802; hg19: chr11-115043888;