8-56444175-T-C

Variant names:

• chr8-56444175-T-C
• rs1437277
• NM_001135690.3:c.138+1641A>G

Variant summary

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

The NM_001135690.3(PENK):​c.138+1641A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,226 control chromosomes in the GnomAD database, including 52,223 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 0.83 (52223 hom., cov: 33)
• Consequence: PENK NM_001135690.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857
• Publications: 5 publications found

Genes affected

PENK (HGNC:8831): (proenkephalin) This gene encodes a preproprotein that is proteolytically processed to generate multiple protein products. These products include the pentapeptide opioids Met-enkephalin and Leu-enkephalin, which are stored in synaptic vesicles, then released into the synapse where they bind to mu- and delta-opioid receptors to modulate the perception of pain. Other non-opioid cleavage products may function in distinct biological activities. [provided by RefSeq, Jul 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PENK	NM_001135690.3	c.138+1641A>G		intron_variant	Intron 3 of 3	ENST00000451791.7	NP_001129162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PENK	ENST00000451791.7	c.138+1641A>G		intron_variant	Intron 3 of 3	1	NM_001135690.3	ENSP00000400894.2

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125490 AN: 152108 Hom.: 52167 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.825 AC: 125608 AN: 152226 Hom.: 52223 Cov.: 33 AF XY: 0.825 AC XY: 61442 AN XY: 74436

African (AFR) AF: 0.928 AC: 38552 AN: 41540

American (AMR) AF: 0.826 AC: 12641 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2766 AN: 3468

East Asian (EAS) AF: 0.870 AC: 4505 AN: 5178

South Asian (SAS) AF: 0.848 AC: 4094 AN: 4826

European-Finnish (FIN) AF: 0.801 AC: 8486 AN: 10596

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51863 AN: 68004

Other (OTH) AF: 0.820 AC: 1727 AN: 2106

Alfa AF: 0.789 Hom.: 66568

Bravo AF: 0.832

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.86
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: rs1437277; hg19: chr8-57356734;