rs7950069

Variant names:

• chr11-115269833-G-A
• rs7950069
• NM_001301043.2:c.125-29413C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-115269833-G-A
• chr11-115269833-G-C
• chr11-115269833-G-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.125-29413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,062 control chromosomes in the GnomAD database, including 7,962 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 0.29 (7962 hom., cov: 32)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.125-29413C>T		intron_variant	Intron 1 of 11	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.125-29413C>T		intron_variant	Intron 1 of 11	1	NM_001301043.2	ENSP00000329797.6

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44167 AN: 151944 Hom.: 7947 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.291 AC: 44227 AN: 152062 Hom.: 7962 Cov.: 32 AF XY: 0.299 AC XY: 22251 AN XY: 74322

African (AFR) AF: 0.456 AC: 18896 AN: 41446

American (AMR) AF: 0.320 AC: 4894 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3466

East Asian (EAS) AF: 0.645 AC: 3343 AN: 5182

South Asian (SAS) AF: 0.218 AC: 1048 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2704 AN: 10552

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11592 AN: 67990

Other (OTH) AF: 0.286 AC: 604 AN: 2114

Alfa AF: 0.212 Hom.: 18758

Bravo AF: 0.304

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.30
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: rs7950069; hg19: chr11-115140553; COSMIC: COSV59010375;