rs2374735

Positions:

• chr7-94511914-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

CASD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASD1	NM_022900.5	c.133+1697A>G		intron_variant		ENST00000297273.9	NP_075051.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASD1	ENST00000297273.9	c.133+1697A>G		intron_variant		1	NM_022900.5	ENSP00000297273.4
CASD1	ENST00000447923.5	c.-75+2615A>G		intron_variant		4		ENSP00000396261.1
CASD1	ENST00000417387.1	n.147+1697A>G		intron_variant		3
CASD1	ENST00000443644.1	n.133+1697A>G		intron_variant		5		ENSP00000389718.1

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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.543

Alfa AF: 0.569 Hom.: 36640

Bravo AF: 0.500

Asia WGS AF: 0.684 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs2374735; hg19: chr7-94141226;