rs7833231

Variant names:

• chr8-4824900-G-A
• rs7833231
• NM_033225.6:c.85+169432C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033225.6(CSMD1):​c.85+169432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,954 control chromosomes in the GnomAD database, including 33,404 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 0.66 (33404 hom., cov: 33)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 2 publications found

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]

PAICSP4 (HGNC:38097): (phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.85+169432C>T		intron_variant	Intron 1 of 69	ENST00000635120.2	NP_150094.5
PAICSP4		n.4824900G>A		intragenic_variant
CSMD1	XM_011534752.3	c.85+169432C>T		intron_variant	Intron 1 of 68		XP_011533054.1
CSMD1	XM_017013731.2	c.85+169432C>T		intron_variant	Intron 1 of 63		XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.85+169432C>T		intron_variant	Intron 1 of 69	5	NM_033225.6	ENSP00000489225.1

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100022 AN: 151836 Hom.: 33379 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.659 AC: 100093 AN: 151954 Hom.: 33404 Cov.: 33 AF XY: 0.666 AC XY: 49484 AN XY: 74296

African (AFR) AF: 0.581 AC: 24085 AN: 41464

American (AMR) AF: 0.770 AC: 11729 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4687 AN: 5172

South Asian (SAS) AF: 0.627 AC: 3024 AN: 4822

European-Finnish (FIN) AF: 0.693 AC: 7330 AN: 10576

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44723 AN: 67898

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

Alfa AF: 0.657 Hom.: 63776

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.82
PhyloP100		-0.026
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7833231; hg19: chr8-4682422;