rs17079506

chr8-3162901-T-A

Variant summary

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

The NM_033225.6(CSMD1):c.5726-624A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,250 control chromosomes in the GnomAD database, including 761 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 0.066 (761 hom., cov: 32)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.5726-624A>T		intron_variant		ENST00000635120.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.5726-624A>T		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9982 AN: 152132 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.00923

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0655

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

GnomAD4 genome AF: 0.0657 AC: 10000 AN: 152250 Hom.: 761 Cov.: 32 AF XY: 0.0644 AC XY: 4797 AN XY: 74464

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.00923

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0648

Alfa AF: 0.0431 Hom.: 60

Bravo AF: 0.0738

Asia WGS AF: 0.0280 AC: 101 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.14
Dann	Benign	0.74

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: rs17079506; hg19: chr8-3020423;