Variant 8-3859946-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_033225.6(CSMD1):c.819-105904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,958 control chromosomes in the GnomAD database, including 12,128 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 0.39 ( 12128 hom., cov: 32)

Consequence

CSMD1
NM_033225.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.432

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]

CSMD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CSMD1	NM_033225.6 link	c.819-105904T>C	intron_variant	ENST00000635120.2	NP_150094.5	Q96PZ7-1Q59FF8
CSMD1	XM_011534752.3 link	c.819-105904T>C	intron_variant		XP_011533054.1
CSMD1	XM_017013731.2 link	c.819-105904T>C	intron_variant		XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2 link	c.819-105904T>C		intron_variant		5	NM_033225.6	ENSP00000489225.1		Q96PZ7-1

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59386

AN:

151838

Hom.:

12103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.414

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

GnomAD4 genome

AF:

0.391

AC:

59453

AN:

151958

Hom.:

12128

Cov.:

AF XY:

0.387

AC XY:

28714

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.486

Gnomad4 AMR

AF:

0.374

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.259

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.416

Alfa

AF:

0.358

Hom.:

16347

Bravo

AF:

0.402

Asia WGS

AF:

0.500

AC:

1739

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.74

DANN

Benign

0.51

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over