rs9657371

chr8-4925136-C-A

Variant summary

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

The NM_033225.6(CSMD1):c.85+69196G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,132 control chromosomes in the GnomAD database, including 7,483 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 0.30 (7483 hom., cov: 30)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.85+69196G>T		intron_variant		ENST00000635120.2
CSMD1	XM_011534752.3	c.85+69196G>T		intron_variant
CSMD1	XM_017013731.2	c.85+69196G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.85+69196G>T		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44776 AN: 151028 Hom.: 7487 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.296 AC: 44804 AN: 151132 Hom.: 7483 Cov.: 30 AF XY: 0.293 AC XY: 21602 AN XY: 73680

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.0422

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.317

Alfa AF: 0.372 Hom.: 22235

Bravo AF: 0.285

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs9657371; hg19: chr8-4782658;