rs6463213

Variant names:

• chr7-4993918-T-A
• rs6463213
• ENST00000407184.5:c.-45+8843T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-4993918-T-A
• chr7-4993918-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

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]

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

ENSG00000288633 (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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407184.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF216P1	NR_015449.1		n.698-2692T>A		intron	N/A
	RNF216P1	NR_023384.1		n.763-1557T>A		intron	N/A
	RNF216P1	NR_023385.1		n.583-2692T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBAK-RBAKDN	ENST00000407184.5	TSL:2	c.-45+8843T>A		intron	N/A	ENSP00000385560.1	I3L0D1
	RNF216P1	ENST00000403969.5	TSL:1	n.518-2692T>A		intron	N/A
	RNF216P1	ENST00000404006.5	TSL:1	n.646-2692T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 472564 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 231714

African (AFR) AF: 0.00 AC: 0 AN: 10946

American (AMR) AF: 0.00 AC: 0 AN: 7256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10304

East Asian (EAS) AF: 0.00 AC: 0 AN: 23276

South Asian (SAS) AF: 0.00 AC: 0 AN: 6344

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30082

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1704

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 359630

Other (OTH) AF: 0.00 AC: 0 AN: 23022

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6463213;

hg19: chr7-5033549;