rs12672177

chr7-102386338-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038967.1(LOC100630923):n.911+10016G>A variant causes a intron, non coding transcript 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: LOC100630923 NR_038967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC100630923	NR_038967.1	n.911+10016G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKRIP1	ENST00000477886.5	n.778+10016G>A		intron_variant, non_coding_transcript_variant		1
PRKRIP1	ENST00000482549.5	n.858+10016G>A		intron_variant, non_coding_transcript_variant		1
PRKRIP1	ENST00000496391.5	c.-435-9639G>A		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.169

Alfa AF: 0.181 Hom.: 1241

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs12672177; hg19: chr7-102026785;