6-36323317-G-T

Position:

• chr6-36323317-G-T

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNIP5	NM_001010903.5	c.1447C>A	p.Arg483Arg	synonymous_variant	8/12	ENST00000437635.3	NP_001010903.3
BNIP5	XM_011514596.3	c.1447C>A	p.Arg483Arg	synonymous_variant	8/12		XP_011512898.1
BNIP5	XM_011514597.3	c.1444C>A	p.Arg482Arg	synonymous_variant	8/12		XP_011512899.1
BNIP5	XM_011514598.3	c.703C>A	p.Arg235Arg	synonymous_variant	7/11		XP_011512900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BNIP5	ENST00000437635.3	c.1447C>A	p.Arg483Arg	synonymous_variant	8/12	1	NM_001010903.5	ENSP00000418983.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs193920980; hg19: chr6-36291094;