rs4875372

Positions:

• chr8-4634998-C-A
• chr8-4634998-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033225.6(CSMD1):​c.302+2344G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,026 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.302+2344G>T		intron_variant		ENST00000635120.2
CSMD1	XM_011534752.3	c.302+2344G>T		intron_variant
CSMD1	XM_017013731.2	c.302+2344G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.302+2344G>T		intron_variant		5	NM_033225.6	P4
	ENST00000647648.1	n.329C>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20251 AN: 151908 Hom.: 1419 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.133 AC: 20270 AN: 152026 Hom.: 1423 Cov.: 33 AF XY: 0.130 AC XY: 9689 AN XY: 74308

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0967

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.136

Alfa AF: 0.136 Hom.: 2057

Bravo AF: 0.129

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4875372; hg19: chr8-4492520;