6-36323317-G-T

Variant names:

• chr6-36323317-G-T
• rs193920980
• NM_001010903.5:c.1447C>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001010903.5(BNIP5):​c.1447C>A​(p.Arg483Arg) variant causes a synonymous 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: BNIP5 NM_001010903.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 8 publications found

Genes affected

BNIP5 (HGNC:33769): (BCL2 interacting protein 5)

ENSG00000297259 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP7: Synonymous conserved (PhyloP=0.656 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010903.5. 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
	BNIP5	NM_001010903.5	MANE Select	c.1447C>A	p.Arg483Arg	synonymous	Exon 8 of 12	NP_001010903.3	P0C671

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNIP5	ENST00000437635.3	TSL:1 MANE Select	c.1447C>A	p.Arg483Arg	synonymous	Exon 8 of 12	ENSP00000418983.1	P0C671
	BNIP5	ENST00000860604.1		c.1444C>A	p.Arg482Arg	synonymous	Exon 8 of 12	ENSP00000530663.1
	BNIP5	ENST00000860607.1		c.1366C>A	p.Arg456Arg	synonymous	Exon 8 of 12	ENSP00000530666.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs193920980; hg19: chr6-36291094;