rs7013027

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033225.6(CSMD1):​c.7475-13800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,046 control chromosomes in the GnomAD database, including 17,753 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 0.48 ( 17753 hom., cov: 32)

Consequence

CSMD1
NM_033225.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CSMD1NM_033225.6 linkuse as main transcriptc.7475-13800T>C intron_variant ENST00000635120.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CSMD1ENST00000635120.2 linkuse as main transcriptc.7475-13800T>C intron_variant 5 NM_033225.6 P4Q96PZ7-1

Frequencies

GnomAD3 genomes
AF:
0.477
AC:
72491
AN:
151928
Hom.:
17751
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.380
Gnomad AMI
AF:
0.522
Gnomad AMR
AF:
0.519
Gnomad ASJ
AF:
0.389
Gnomad EAS
AF:
0.383
Gnomad SAS
AF:
0.386
Gnomad FIN
AF:
0.621
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.447
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.477
AC:
72513
AN:
152046
Hom.:
17753
Cov.:
32
AF XY:
0.480
AC XY:
35674
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.380
Gnomad4 AMR
AF:
0.518
Gnomad4 ASJ
AF:
0.389
Gnomad4 EAS
AF:
0.382
Gnomad4 SAS
AF:
0.386
Gnomad4 FIN
AF:
0.621
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.442
Alfa
AF:
0.506
Hom.:
21461
Bravo
AF:
0.465
Asia WGS
AF:
0.350
AC:
1216
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.5
DANN
Benign
0.50

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7013027; hg19: chr8-2923969; API