NM_004331.3:c.284+1740C>T

Variant names:

• chr8-26393166-C-T
• rs3808579
• NM_004331.3:c.284+1740C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004331.3(BNIP3L):​c.284+1740C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,600 control chromosomes in the GnomAD database, including 38,366 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 0.71 (38366 hom., cov: 28)
• Consequence: BNIP3L NM_004331.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 4 publications found

Genes affected

BNIP3L (HGNC:1085): (BCL2 interacting protein 3 like) This gene encodes a protein that belongs to the pro-apoptotic subfamily within the Bcl-2 family of proteins. The encoded protein binds to Bcl-2 and possesses the BH3 domain. The protein directly targets mitochondria and causes apoptotic changes, including loss of membrane potential and the release of cytochrome c. [provided by RefSeq, Feb 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNIP3L	NM_004331.3	c.284+1740C>T		intron_variant	Intron 2 of 5	ENST00000380629.7	NP_004322.1
BNIP3L	NM_001330491.2	c.164+1740C>T		intron_variant	Intron 2 of 5		NP_001317420.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BNIP3L	ENST00000380629.7	c.284+1740C>T		intron_variant	Intron 2 of 5	1	NM_004331.3	ENSP00000370003.2

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107375 AN: 151482 Hom.: 38320 Cov.: 28

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.694

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.709 AC: 107476 AN: 151600 Hom.: 38366 Cov.: 28 AF XY: 0.713 AC XY: 52788 AN XY: 74056

African (AFR) AF: 0.727 AC: 29993 AN: 41280

American (AMR) AF: 0.643 AC: 9786 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4501 AN: 5136

South Asian (SAS) AF: 0.741 AC: 3541 AN: 4780

European-Finnish (FIN) AF: 0.778 AC: 8177 AN: 10508

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47200 AN: 67902

Other (OTH) AF: 0.698 AC: 1464 AN: 2098

Alfa AF: 0.697 Hom.: 5497

Bravo AF: 0.696

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.71
PhyloP100		-0.0050
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3808579; hg19: chr8-26250682;