11-114402196-A-T

Variant names:

• chr11-114402196-A-T
• NM_001286045.2:c.259+336A>T

Variant summary

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

The NM_001286045.2(RBM7):​c.259+336A>T variant causes a intron 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: RBM7 NM_001286045.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 0 publications found

Genes affected

RBM7 (HGNC:9904): (RNA binding motif protein 7) Enables 14-3-3 protein binding activity; pre-mRNA intronic binding activity; and snRNA binding activity. Involved in snRNA catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255663 (HGNC:):

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=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286045.2. 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
	RBM7	NM_001286045.2	MANE Select	c.259+336A>T		intron	N/A	NP_001272974.1
	RBM7	NM_016090.4		c.259+336A>T		intron	N/A	NP_057174.1
	RBM7	NM_001286046.2		c.-101+336A>T		intron	N/A	NP_001272975.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM7	ENST00000375490.10	TSL:1 MANE Select	c.259+336A>T		intron	N/A	ENSP00000364639.5
	RBM7	ENST00000540163.5	TSL:1	c.259+336A>T		intron	N/A	ENSP00000439918.1
	RBM7	ENST00000542140.5	TSL:1	n.259+336A>T		intron	N/A	ENSP00000437998.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		-0.023

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

hg19: chr11-114272918;