8-3101140-G-A

Position:

• chr8-3101140-G-A

Variant summary

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

The NM_033225.6(CSMD1):​c.6950-4103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 150,612 control chromosomes in the GnomAD database, including 153 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 0.041 (153 hom., cov: 30)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.6950-4103C>T		intron_variant		ENST00000635120.2	NP_150094.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.6950-4103C>T		intron_variant		5	NM_033225.6	ENSP00000489225	P4

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6150 AN: 150502 Hom.: 152 Cov.: 30

Gnomad AFR AF: 0.00919

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0533

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0409 AC: 6154 AN: 150612 Hom.: 153 Cov.: 30 AF XY: 0.0408 AC XY: 2992 AN XY: 73406

Gnomad4 AFR AF: 0.00916

Gnomad4 AMR AF: 0.0687

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0533

Gnomad4 OTH AF: 0.0476

Alfa AF: 0.0518 Hom.: 130

Bravo AF: 0.0424

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.43

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: rs17390295; hg19: chr8-2958662;