rs779107

Positions:

• chr8-4261554-C-A
• chr8-4261554-C-G

Variant summary

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

The NM_033225.6(CSMD1):​c.415+158399G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,872 control chromosomes in the GnomAD database, including 16,351 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 0.44 (16351 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.415+158399G>T		intron_variant		ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.415+158399G>T		intron_variant			XP_011533054.1
CSMD1	XM_017013731.2	c.415+158399G>T		intron_variant			XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.415+158399G>T		intron_variant		5	NM_033225.6	ENSP00000489225	P4

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66136 AN: 151754 Hom.: 16359 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.435 AC: 66133 AN: 151872 Hom.: 16351 Cov.: 31 AF XY: 0.436 AC XY: 32357 AN XY: 74226

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.464

Alfa AF: 0.497 Hom.: 4688

Bravo AF: 0.410

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.24

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: rs779107; hg19: chr8-4119076;