rs2374735

Variant names:

• chr7-94511914-A-G
• rs2374735
• NM_022900.5:c.133+1697A>G

Variant summary

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

The NM_022900.5(CASD1):​c.133+1697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,056 control chromosomes in the GnomAD database, including 21,240 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 0.51 (21240 hom., cov: 32)
• Consequence: CASD1 NM_022900.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 5 publications found

Genes affected

CASD1 (HGNC:16014): (CAS1 domain containing 1) Enables N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity. Involved in carbohydrate metabolic process. Is integral component of Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000309657 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022900.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASD1	NM_022900.5	MANE Select	c.133+1697A>G		intron	N/A	NP_075051.4
	CASD1	NM_001363426.1		c.-490+1697A>G		intron	N/A	NP_001350355.1
	CASD1	NM_001363428.1		c.-439+1697A>G		intron	N/A	NP_001350357.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASD1	ENST00000297273.9	TSL:1 MANE Select	c.133+1697A>G		intron	N/A	ENSP00000297273.4	Q96PB1
	CASD1	ENST00000919855.1		c.133+1697A>G		intron	N/A	ENSP00000589914.1
	CASD1	ENST00000919856.1		c.133+1697A>G		intron	N/A	ENSP00000589915.1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78069 AN: 151938 Hom.: 21221 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.514 AC: 78121 AN: 152056 Hom.: 21240 Cov.: 32 AF XY: 0.517 AC XY: 38372 AN XY: 74290

African (AFR) AF: 0.326 AC: 13507 AN: 41472

American (AMR) AF: 0.545 AC: 8332 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3547 AN: 5176

South Asian (SAS) AF: 0.726 AC: 3500 AN: 4818

European-Finnish (FIN) AF: 0.583 AC: 6159 AN: 10566

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39477 AN: 67954

Other (OTH) AF: 0.543 AC: 1148 AN: 2114

Alfa AF: 0.554 Hom.: 65801

Bravo AF: 0.500

Asia WGS AF: 0.684 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.9
DANN	Benign	0.74
PhyloP100		-0.37
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

Other links and lift over

dbSNP: rs2374735; hg19: chr7-94141226;