rs2822445

Variant names:

• chr21-14227444-T-A
• rs2822445
• ENST00000468643.5:n.1064T>A

Your query was ambiguous. Multiple possible variants found:

• chr21-14227444-T-A
• chr21-14227444-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000468643.5(RBM11):​n.1064T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RBM11 ENST00000468643.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• Publications: 8 publications found

Genes affected

RBM11 (HGNC:9897): (RNA binding motif protein 11) Enables poly(U) RNA binding activity and protein homodimerization activity. Acts upstream of or within cellular response to oxidative stress and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM11	NM_144770.5	c.*151T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000400577.4	NP_658983.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM11	ENST00000468643.5	n.1064T>A		non_coding_transcript_exon_variant	Exon 5 of 5	1
RBM11	ENST00000495055.1	n.868T>A		non_coding_transcript_exon_variant	Exon 4 of 4	1
RBM11	ENST00000400577.4	c.*151T>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_144770.5	ENSP00000383421.3
RBM11	ENST00000475864.1	n.*60T>A		downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.88
PhyloP100		0.82

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: rs2822445; hg19: chr21-15599765;