NM_138278.4:c.1037+220A>G

Variant names:

• chr1-151046385-A-G
• rs6587552
• NM_138278.4:c.1037+220A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BNIPL	NM_138278.4	c.1037+220A>G		intron_variant	Intron 9 of 9	ENST00000368931.8	NP_612122.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BNIPL	ENST00000368931.8	c.1037+220A>G		intron_variant	Intron 9 of 9	1	NM_138278.4	ENSP00000357927.3

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

African (AFR) AF: 0.502 AC: 20698 AN: 41208

American (AMR) AF: 0.749 AC: 11423 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2785 AN: 3466

East Asian (EAS) AF: 0.888 AC: 4597 AN: 5178

South Asian (SAS) AF: 0.732 AC: 3504 AN: 4784

European-Finnish (FIN) AF: 0.733 AC: 7579 AN: 10340

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.765 AC: 51897 AN: 67860

Other (OTH) AF: 0.735 AC: 1544 AN: 2102

Alfa AF: 0.745 Hom.: 165552

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
PhyloP100		-0.069
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6587552; hg19: chr1-151018861;