rs1499693

Positions:

• chr8-3431928-T-C
• chr8-3431928-T-G

Variant summary

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

The NM_033225.6(CSMD1):​c.1562-22323A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,120 control chromosomes in the GnomAD database, including 37,557 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 0.70 (37557 hom., cov: 34)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.1562-22323A>G		intron_variant		ENST00000635120.2
CSMD1	XM_011534752.3	c.1562-22323A>G		intron_variant
CSMD1	XM_017013731.2	c.1562-22323A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.1562-22323A>G		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106422 AN: 152002 Hom.: 37549 Cov.: 34

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.700 AC: 106472 AN: 152120 Hom.: 37557 Cov.: 34 AF XY: 0.699 AC XY: 51997 AN XY: 74376

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.706

Alfa AF: 0.733 Hom.: 80259

Bravo AF: 0.696

Asia WGS AF: 0.633 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.30

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: rs1499693; hg19: chr8-3289450;