rs2235316

Variant names:

• chr22-43127985-C-A
• rs2235316
• NM_001197.5:c.260+190C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-43127985-C-A
• chr22-43127985-C-G
• chr22-43127985-C-T

Variant summary

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

The NM_001197.5(BIK):​c.260+190C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,852 control chromosomes in the GnomAD database, including 23,247 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 0.50 (23247 hom., cov: 32)
• Consequence: BIK NM_001197.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 publications found

Genes affected

BIK (HGNC:1051): (BCL2 interacting killer) The protein encoded by this gene shares a critical BH3 domain with other death-promoting proteins, such as BID, BAK, BAD and BAX, that is required for its pro-apoptotic activity, and for interaction with anti-apoptotic members of the BCL2 family, and viral survival-promoting proteins. Since the activity of this protein is suppressed in the presence of survival-promoting proteins, it is suggested as a likely target for anti-apoptotic proteins. [provided by RefSeq, Sep 2011]

BIK Gene-Disease associations (from GenCC):

• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001197.5. 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
	BIK	NM_001197.5	MANE Select	c.260+190C>A		intron	N/A	NP_001188.1	Q13323

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIK	ENST00000216115.3	TSL:1 MANE Select	c.260+190C>A		intron	N/A	ENSP00000216115.2	Q13323
	BIK	ENST00000918052.1		c.260+190C>A		intron	N/A	ENSP00000588111.1
	BIK	ENST00000910665.1		c.260+190C>A		intron	N/A	ENSP00000580724.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76488 AN: 151734 Hom.: 23247 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.504 AC: 76503 AN: 151852 Hom.: 23247 Cov.: 32 AF XY: 0.502 AC XY: 37293 AN XY: 74216

African (AFR) AF: 0.150 AC: 6215 AN: 41472

American (AMR) AF: 0.524 AC: 8004 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2718 AN: 5148

South Asian (SAS) AF: 0.509 AC: 2454 AN: 4824

European-Finnish (FIN) AF: 0.694 AC: 7316 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45753 AN: 67824

Other (OTH) AF: 0.539 AC: 1134 AN: 2102

Alfa AF: 0.593 Hom.: 3696

Bravo AF: 0.481

Asia WGS AF: 0.486 AC: 1690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.55
PhyloP100		-1.6
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: rs2235316; hg19: chr22-43523991;