rs12672177

Variant names:

• chr7-102386338-G-A
• rs12672177
• ENST00000477886.5:n.778+10016G>A

Variant summary

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

The ENST00000477886.5(PRKRIP1):​n.778+10016G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,172 control chromosomes in the GnomAD database, including 2,937 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 0.17 (2937 hom., cov: 33)
• Consequence: PRKRIP1 ENST00000477886.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 5 publications found

Genes affected

PRKRIP1 (HGNC:21894): (PRKR interacting protein 1) Predicted to enable double-stranded RNA binding activity; protein kinase binding activity; and protein kinase inhibitor activity. Involved in renal system process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

LOC100630923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100630923	NR_038967.1	n.911+10016G>A		intron_variant	Intron 4 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKRIP1	ENST00000477886.5	n.778+10016G>A		intron_variant	Intron 3 of 5	1
PRKRIP1	ENST00000482549.5	n.858+10016G>A		intron_variant	Intron 4 of 8	1
PRKRIP1	ENST00000496391.5	c.-435-9639G>A		intron_variant	Intron 4 of 9	2		ENSP00000419270.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26127 AN: 152054 Hom.: 2940 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.172 AC: 26119 AN: 152172 Hom.: 2937 Cov.: 33 AF XY: 0.178 AC XY: 13262 AN XY: 74390

African (AFR) AF: 0.0395 AC: 1639 AN: 41544

American (AMR) AF: 0.273 AC: 4172 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1826 AN: 5192

South Asian (SAS) AF: 0.148 AC: 712 AN: 4826

European-Finnish (FIN) AF: 0.271 AC: 2861 AN: 10566

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13491 AN: 68002

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.164 Hom.: 1462

Bravo AF: 0.165

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.80
PhyloP100		-0.93
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: rs12672177; hg19: chr7-102026785;