rs12164179

Variant names:

• chr8-26433920-A-C
• rs12164179
• ENST00000515686.1:n.146T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-26433920-A-C
• chr8-26433920-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000515686.1(DNAJB6P2):​n.146T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DNAJB6P2 ENST00000515686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 1 publications found

Genes affected

DNAJB6P2 (HGNC:54755): (DNAJB6 pseudogene 2)

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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJB6P2		n.26433920A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJB6P2	ENST00000515686.1	n.146T>G		non_coding_transcript_exon_variant	Exon 1 of 2	6
BNIP3L	ENST00000523949.5	c.545+25544A>C		intron_variant	Intron 5 of 5	3		ENSP00000429171.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 598634 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 326470

African (AFR) AF: 0.00 AC: 0 AN: 16684

American (AMR) AF: 0.00 AC: 0 AN: 41304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19794

East Asian (EAS) AF: 0.00 AC: 0 AN: 34228

South Asian (SAS) AF: 0.00 AC: 0 AN: 68346

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37044

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2322

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 347752

Other (OTH) AF: 0.00 AC: 0 AN: 31160

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.4
DANN	Benign	0.29
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12164179; hg19: chr8-26291436;