NM_138278.4:c.256C>T

Variant names:

• chr1-151038849-C-T
• rs61751619
• NM_138278.4:c.256C>T

Variant summary

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

The NM_138278.4(BNIPL):​c.256C>T​(p.Arg86Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,613,130 control chromosomes in the GnomAD database, including 15,263 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R86H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.095 (965 hom., cov: 32)
  • Exomes 𝑓: 0.13 (14298 hom.)
• Consequence: BNIPL NM_138278.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• 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 (MetaRNN=0.0017173588).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138278.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNIPL	NM_138278.4	MANE Select	c.256C>T	p.Arg86Cys	missense	Exon 4 of 10	NP_612122.2	Q7Z465-1
	BNIPL	NM_001159642.2		c.10C>T	p.Arg4Cys	missense	Exon 4 of 10	NP_001153114.1	Q7Z465-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNIPL	ENST00000368931.8	TSL:1 MANE Select	c.256C>T	p.Arg86Cys	missense	Exon 4 of 10	ENSP00000357927.3	Q7Z465-1
	BNIPL	ENST00000295294.11	TSL:1	c.10C>T	p.Arg4Cys	missense	Exon 4 of 10	ENSP00000295294.7	Q7Z465-2
	BNIPL	ENST00000912274.1		c.256C>T	p.Arg86Cys	missense	Exon 4 of 10	ENSP00000582333.1

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14544 AN: 152194 Hom.: 965 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.100

GnomAD2 exomes AF: 0.0991 AC: 24820 AN: 250470 AF XY: 0.102

Gnomad AFR exome AF: 0.0210

Gnomad AMR exome AF: 0.0497

Gnomad ASJ exome AF: 0.109

Gnomad EAS exome AF: 0.000272

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.145

Gnomad OTH exome AF: 0.0964

GnomAD4 exome AF: 0.133 AC: 194981 AN: 1460818 Hom.: 14298 Cov.: 32 AF XY: 0.132 AC XY: 95874 AN XY: 726688

African (AFR) AF: 0.0194 AC: 649 AN: 33442

American (AMR) AF: 0.0520 AC: 2313 AN: 44512

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 2849 AN: 26078

East Asian (EAS) AF: 0.000227 AC: 9 AN: 39688

South Asian (SAS) AF: 0.0729 AC: 6281 AN: 86198

European-Finnish (FIN) AF: 0.116 AC: 6178 AN: 53390

Middle Eastern (MID) AF: 0.0720 AC: 415 AN: 5762

European-Non Finnish (NFE) AF: 0.152 AC: 169464 AN: 1111400

Other (OTH) AF: 0.113 AC: 6823 AN: 60348

GnomAD4 genome AF: 0.0955 AC: 14541 AN: 152312 Hom.: 965 Cov.: 32 AF XY: 0.0917 AC XY: 6831 AN XY: 74490

African (AFR) AF: 0.0261 AC: 1084 AN: 41576

American (AMR) AF: 0.0787 AC: 1204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3472

East Asian (EAS) AF: 0.000962 AC: 5 AN: 5196

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4828

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10602

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 9988 AN: 68026

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.123 Hom.: 3077

Bravo AF: 0.0899

TwinsUK AF: 0.157 AC: 582

ALSPAC AF: 0.154 AC: 594

ESP6500AA AF: 0.0306 AC: 135

ESP6500EA AF: 0.142 AC: 1221

ExAC AF: 0.0999 AC: 12129

Asia WGS AF: 0.0330 AC: 117 AN: 3478

EpiCase AF: 0.141

EpiControl AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.44	T
BayesDel_noAF	Benign	-0.27
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.11	T
Eigen	Pathogenic	0.71
Eigen_PC	Pathogenic	0.66
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.85	T
MetaRNN	Benign	0.0017	T
MetaSVM	Benign	-0.43	T
MutationAssessor	Uncertain	2.6	M
PhyloP100		2.1
PrimateAI	Uncertain	0.55	T
PROVEAN	Uncertain	-4.0	D
REVEL	Benign	0.21
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.13
MPC		1.2
ClinPred		0.021	T
GERP RS		5.2
PromoterAI		-0.050	Neutral
Varity_R		0.36
gMVP		0.18
Mutation Taster		=97/3	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs61751619; hg19: chr1-151011325; COSMIC: COSV107228884; COSMIC: COSV107228884;