rs1382249

Variant names:

• chr8-4600690-G-A
• rs1382249
• NM_033225.6:c.302+36652C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-4600690-G-A
• chr8-4600690-G-C
• chr8-4600690-G-T

Variant summary

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

The NM_033225.6(CSMD1):​c.302+36652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,062 control chromosomes in the GnomAD database, including 49,118 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 0.80 (49118 hom., cov: 32)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731
• Publications: 2 publications found

Genes affected

CSMD1 (HGNC:14026): (CUB and Sushi multiple domains 1) Predicted to act upstream of or within several processes, including learning or memory; mammary gland branching involved in pregnancy; and reproductive structure development. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CSMD1 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AR 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.302+36652C>T		intron_variant	Intron 2 of 69	ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.302+36652C>T		intron_variant	Intron 2 of 68		XP_011533054.1
CSMD1	XM_017013731.2	c.302+36652C>T		intron_variant	Intron 2 of 63		XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.302+36652C>T		intron_variant	Intron 2 of 69	5	NM_033225.6	ENSP00000489225.1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121201 AN: 151944 Hom.: 49117 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.960

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.797 AC: 121241 AN: 152062 Hom.: 49118 Cov.: 32 AF XY: 0.799 AC XY: 59368 AN XY: 74322

African (AFR) AF: 0.644 AC: 26663 AN: 41424

American (AMR) AF: 0.787 AC: 12028 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3064 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4409 AN: 5144

South Asian (SAS) AF: 0.822 AC: 3959 AN: 4816

European-Finnish (FIN) AF: 0.871 AC: 9235 AN: 10600

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59048 AN: 68012

Other (OTH) AF: 0.814 AC: 1718 AN: 2110

Alfa AF: 0.849 Hom.: 87351

Bravo AF: 0.785

Asia WGS AF: 0.820 AC: 2847 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		0.73
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: rs1382249; hg19: chr8-4458212;