chr21-14227444-T-A

Variant names:

• chr21-14227444-T-A
• rs2822445
• NM_144770.5:c.*151T>A

Variant summary

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

The NM_001320602.2(RBM11):​c.*151T>A variant causes a 3 prime UTR 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 NM_001320602.2 3_prime_UTR
• 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320602.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM11	NM_144770.5	MANE Select	c.*151T>A		3_prime_UTR	Exon 5 of 5	NP_658983.3
	RBM11	NM_001320602.2		c.*151T>A		3_prime_UTR	Exon 5 of 5	NP_001307531.1
	RBM11	NR_135308.2		n.864T>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM11	ENST00000400577.4	TSL:1 MANE Select	c.*151T>A		3_prime_UTR	Exon 5 of 5	ENSP00000383421.3
	RBM11	ENST00000468643.5	TSL:1	n.1064T>A		non_coding_transcript_exon	Exon 5 of 5
	RBM11	ENST00000495055.1	TSL:1	n.868T>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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;