Genetic Variant RBAK-RBAKDN:c.-45+8843T>A (chr7-4993918-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000407184.5(RBAK-RBAKDN):c.-45+8843T>A 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: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RBAK-RBAKDN
ENST00000407184.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

1 publications found

Variant links:

Genes affected

RBAK-RBAKDN (HGNC:42971): (RBAK-RBAKDN readthrough) This locus represents naturally occurring read-through transcription between the neighboring RBAK (RB-associated KRAB zinc finger) and LOC389458 (hypothetical LOC389458) genes on chromosome 7. The read-through transcript encodes a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to frameshifts relative to the downstream gene. [provided by RefSeq, Mar 2011]

RBAK-RBAKDN links:

RNF216P1 (HGNC:33610): (ring finger protein 216 pseudogene 1)

RNF216P1 links:

ENSG00000288633 (HGNC:):

ENSG00000288633 links:

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ACMG classification

Classification was made for transcript

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
RNF216P1	NR_015449.1 link	n.698-2692T>A	intron_variant	Intron 5 of 5
RNF216P1	NR_023384.1 link	n.763-1557T>A	intron_variant	Intron 6 of 7
RNF216P1	NR_023385.1 link	n.583-2692T>A	intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBAK-RBAKDN	ENST00000407184.5 link	c.-45+8843T>A		intron_variant	Intron 2 of 7	2		ENSP00000385560.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

472564

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

231714

African (AFR)

AF:

0.00

AC:

AN:

10946

American (AMR)

AF:

0.00

AC:

AN:

7256

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10304

East Asian (EAS)

AF:

0.00

AC:

AN:

23276

South Asian (SAS)

AF:

0.00

AC:

AN:

6344

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30082

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1704

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

359630

Other (OTH)

AF:

0.00

AC:

AN:

23022

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.9

(source)

DANN

Benign

0.29

PhyloP100

-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over