8-26433920-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515686.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB6P2	ENST00000515686.1	TSL:6	n.146T>C		non_coding_transcript_exon	Exon 1 of 2
	BNIP3L	ENST00000523949.5	TSL:3	c.545+25544A>G		intron	N/A	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 v4.9

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;