rs7759666

Variant names:

• chr6-30601712-C-A
• rs7759666
• NM_002714.4:c.2714-54G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-30601712-C-A
• chr6-30601712-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002714.4(PPP1R10):​c.2714-54G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PPP1R10 NM_002714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 15 publications found

Genes affected

PPP1R10 (HGNC:9284): (protein phosphatase 1 regulatory subunit 10) This gene encodes a protein phosphatase 1 binding protein. The encoded protein plays a role in many cellular processes including cell cycle progression, DNA repair and apoptosis by regulating the activity of protein phosphatase 1. This gene lies within the major histocompatibility complex class I region on chromosome 6, and alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R10	NM_002714.4	c.2714-54G>T		intron_variant	Intron 19 of 19	ENST00000376511.7	NP_002705.2
PPP1R10	NM_001376195.1	c.2714-54G>T		intron_variant	Intron 19 of 19		NP_001363124.1
PPP1R10	NR_072994.2	n.3205-54G>T		intron_variant	Intron 19 of 19
PPP1R10	XM_011514722.2	c.2714-54G>T		intron_variant	Intron 20 of 20		XP_011513024.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R10	ENST00000376511.7	c.2714-54G>T		intron_variant	Intron 19 of 19	1	NM_002714.4	ENSP00000365694.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1331456 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 666408

African (AFR) AF: 0.00 AC: 0 AN: 30748

American (AMR) AF: 0.00 AC: 0 AN: 41620

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24266

East Asian (EAS) AF: 0.00 AC: 0 AN: 38534

South Asian (SAS) AF: 0.00 AC: 0 AN: 81476

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5540

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1002616

Other (OTH) AF: 0.00 AC: 0 AN: 56084

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5821

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7759666; hg19: chr6-30569489;