rs1540507

Positions:

• chr8-3231241-C-T

Variant summary

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

The NM_033225.6(CSMD1):​c.4154-1010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,170 control chromosomes in the GnomAD database, including 762 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 0.087 (762 hom., cov: 33)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.4154-1010G>A		intron_variant		ENST00000635120.2	NP_150094.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.4154-1010G>A		intron_variant		5	NM_033225.6	ENSP00000489225	P4

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13243 AN: 152052 Hom.: 762 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0871 AC: 13261 AN: 152170 Hom.: 762 Cov.: 33 AF XY: 0.0895 AC XY: 6662 AN XY: 74404

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.0534

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0992 Hom.: 1023

Bravo AF: 0.0839

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.64

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: rs1540507; hg19: chr8-3088763;