rs6587552

chr1-151046385-A-Gchr1-151046385-A-T

Variant summary

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

The NM_138278.4(BNIPL):c.1037+220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,390 control chromosomes in the GnomAD database, including 37,589 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 0.69 (37589 hom., cov: 28)
• Consequence: BNIPL NM_138278.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

BNIPL (HGNC:16976): (BCL2 interacting protein like) The protein encoded by this gene interacts with several other proteins, such as BCL2, ARHGAP1, MIF and GFER. It may function as a bridge molecule between BCL2 and ARHGAP1/CDC42 in promoting cell death. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNIPL	NM_138278.4	c.1037+220A>G		intron_variant		ENST00000368931.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNIPL	ENST00000368931.8	c.1037+220A>G		intron_variant		1	NM_138278.4	P1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 104926 AN: 151276 Hom.: 37579 Cov.: 28

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.693 AC: 104972 AN: 151390 Hom.: 37589 Cov.: 28 AF XY: 0.695 AC XY: 51357 AN XY: 73946

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.735

Alfa AF: 0.758 Hom.: 74073

Bravo AF: 0.690

Asia WGS AF: 0.759 AC: 2617 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.25
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6587552; hg19: chr1-151018861;