rs9811920

Positions:

• chr3-100125449-G-A

Variant summary

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

The NM_032359.4(CMSS1):​c.65-21524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,970 control chromosomes in the GnomAD database, including 14,068 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 0.43 (14068 hom., cov: 32)
• Consequence: CMSS1 NM_032359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

CMSS1 (HGNC:28666): (cms1 ribosomal small subunit homolog) Enables RNA binding activity. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMSS1	NM_032359.4	c.65-21524G>A		intron_variant		ENST00000421999.8	NP_115735.2
CMSS1	NM_001167924.2	c.10+10451G>A		intron_variant			NP_001161396.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMSS1	ENST00000421999.8	c.65-21524G>A		intron_variant		1	NM_032359.4	ENSP00000410396.2
CMSS1	ENST00000489081.5	c.10+10451G>A		intron_variant		2		ENSP00000419161.1
CMSS1	ENST00000463526.1	c.-38-21524G>A		intron_variant		3		ENSP00000418855.1
CMSS1	ENST00000491299.5	n.65-16081G>A		intron_variant		5		ENSP00000418609.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64749 AN: 151850 Hom.: 14042 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.427 AC: 64831 AN: 151970 Hom.: 14068 Cov.: 32 AF XY: 0.429 AC XY: 31868 AN XY: 74270

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.404

Alfa AF: 0.395 Hom.: 20368

Bravo AF: 0.426

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.70

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: rs9811920; hg19: chr3-99844293;