chr8-26433920-A-G

Variant names:

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

Variant summary

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

The ENST00000515686.1(DNAJB6P2):​n.146T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 750,336 control chromosomes in the GnomAD database, including 312,141 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 0.91 (63306 hom., cov: 29)
  • Exomes 𝑓: 0.91 (248835 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138408 AN: 151876 Hom.: 63289 Cov.: 29

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.923

GnomAD4 exome AF: 0.909 AC: 543864 AN: 598342 Hom.: 248835 Cov.: 7 AF XY: 0.904 AC XY: 295027 AN XY: 326328

African (AFR) AF: 0.887 AC: 14784 AN: 16672

American (AMR) AF: 0.764 AC: 31533 AN: 41250

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 18928 AN: 19790

East Asian (EAS) AF: 0.852 AC: 29130 AN: 34194

South Asian (SAS) AF: 0.771 AC: 52696 AN: 68312

European-Finnish (FIN) AF: 0.934 AC: 34565 AN: 37026

Middle Eastern (MID) AF: 0.927 AC: 2149 AN: 2318

European-Non Finnish (NFE) AF: 0.953 AC: 331320 AN: 347648

Other (OTH) AF: 0.924 AC: 28759 AN: 31132

GnomAD4 genome AF: 0.911 AC: 138478 AN: 151994 Hom.: 63306 Cov.: 29 AF XY: 0.905 AC XY: 67258 AN XY: 74292

African (AFR) AF: 0.882 AC: 36572 AN: 41446

American (AMR) AF: 0.853 AC: 13019 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3306 AN: 3472

East Asian (EAS) AF: 0.838 AC: 4307 AN: 5138

South Asian (SAS) AF: 0.751 AC: 3600 AN: 4792

European-Finnish (FIN) AF: 0.933 AC: 9862 AN: 10570

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64718 AN: 67996

Other (OTH) AF: 0.920 AC: 1935 AN: 2104

Alfa AF: 0.921 Hom.: 27795

Bravo AF: 0.907

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.5
DANN	Benign	0.21
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;