rs7882

chr15-59659374-A-Gchr15-59659374-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004330.4(BNIP2):c.*4695T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,106 control chromosomes in the GnomAD database, including 24,725 homozygotes. 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: 𝑓 0.56 (24725 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: BNIP2 NM_004330.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

Genes affected

BNIP2 (HGNC:1083): (BCL2 interacting protein 2) This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNIP2	NM_004330.4	c.*4695T>C		3_prime_UTR_variant	10/10	ENST00000607373.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNIP2	ENST00000607373.6	c.*4695T>C		3_prime_UTR_variant	10/10	1	NM_004330.4	P3
	ENST00000441746.1	n.68+12861T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85485 AN: 151984 Hom.: 24713 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.562 AC: 85537 AN: 152102 Hom.: 24725 Cov.: 33 AF XY: 0.553 AC XY: 41116 AN XY: 74336

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.574

Alfa AF: 0.595 Hom.: 12486

Bravo AF: 0.565

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.66
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7882; hg19: chr15-59951573;