rs9811920

Variant names:

• chr3-100125449-G-A
• rs9811920
• NM_032359.4:c.65-21524G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

Genes affected

CMSS1 (HGNC:28666): (cms1 ribosomal small subunit homolog) Enables RNA binding activity. [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=-0.85).
• 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 rank	MANE	Protein	UniProt
CMSS1	NM_032359.4	c.65-21524G>A		intron_variant	Intron 1 of 9	ENST00000421999.8	NP_115735.2
CMSS1	NM_001167924.2	c.10+10451G>A		intron_variant	Intron 1 of 9		NP_001161396.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMSS1	ENST00000421999.8	c.65-21524G>A		intron_variant	Intron 1 of 9	1	NM_032359.4	ENSP00000410396.2
CMSS1	ENST00000489081.5	c.10+10451G>A		intron_variant	Intron 1 of 9	2		ENSP00000419161.1
CMSS1	ENST00000463526.1	c.-38-21524G>A		intron_variant	Intron 2 of 3	3		ENSP00000418855.1
CMSS1	ENST00000491299.5	n.65-16081G>A		intron_variant	Intron 1 of 8	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

African (AFR) AF: 0.486 AC: 20145 AN: 41430

American (AMR) AF: 0.425 AC: 6493 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1838 AN: 5176

South Asian (SAS) AF: 0.469 AC: 2257 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4412 AN: 10552

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27205 AN: 67946

Other (OTH) AF: 0.404 AC: 855 AN: 2116

Alfa AF: 0.405 Hom.: 50720

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
PhyloP100		-0.86
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: rs9811920; hg19: chr3-99844293;