8-3459464-G-A

Position:

• chr8-3459464-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.1561+9248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,154 control chromosomes in the GnomAD database, including 1,419 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 0.14 (1419 hom., cov: 33)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.1561+9248C>T		intron_variant		ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.1561+9248C>T		intron_variant			XP_011533054.1
CSMD1	XM_017013731.2	c.1561+9248C>T		intron_variant			XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.1561+9248C>T		intron_variant		5	NM_033225.6	ENSP00000489225	P4

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20664 AN: 152036 Hom.: 1421 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.136 AC: 20670 AN: 152154 Hom.: 1419 Cov.: 33 AF XY: 0.139 AC XY: 10311 AN XY: 74394

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.125

Alfa AF: 0.136 Hom.: 1482

Bravo AF: 0.132

Asia WGS AF: 0.179 AC: 624 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	0.28
DANN	Benign	0.67

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: rs17394429; hg19: chr8-3316986;