8-3358503-T-G

Variant names:

• chr8-3358503-T-G
• rs9773092
• NM_033225.6:c.3304+649A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033225.6(CSMD1):​c.3304+649A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,084 control chromosomes in the GnomAD database, including 6,395 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 0.28 (6395 hom., cov: 32)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.3304+649A>C		intron_variant	Intron 21 of 69	ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.3304+649A>C		intron_variant	Intron 21 of 68		XP_011533054.1
CSMD1	XM_017013731.2	c.3304+649A>C		intron_variant	Intron 21 of 63		XP_016869220.1
CSMD1	XM_011534753.4	c.397+649A>C		intron_variant	Intron 4 of 52		XP_011533055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.3304+649A>C		intron_variant	Intron 21 of 69	5	NM_033225.6	ENSP00000489225.1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42834 AN: 151968 Hom.: 6383 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.282 AC: 42884 AN: 152084 Hom.: 6395 Cov.: 32 AF XY: 0.276 AC XY: 20491 AN XY: 74340

African (AFR) AF: 0.385 AC: 15972 AN: 41462

American (AMR) AF: 0.316 AC: 4831 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5166

South Asian (SAS) AF: 0.194 AC: 938 AN: 4830

European-Finnish (FIN) AF: 0.161 AC: 1709 AN: 10590

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16070 AN: 67978

Other (OTH) AF: 0.282 AC: 596 AN: 2114

Alfa AF: 0.226 Hom.: 2310

Bravo AF: 0.305

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.048
DANN	Benign	0.42
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs9773092; hg19: chr8-3216025; COSMIC: COSV59338107;