rs1461729

Variant names:

• chr8-9329732-A-C
• rs1461729
• ENST00000518619.1:n.196+3429A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-9329732-A-C
• chr8-9329732-A-G
• chr8-9329732-A-T

Variant summary

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

The ENST00000518619.1(PPP1R3B-DT):​n.196+3429A>C 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)
• Consequence: PPP1R3B-DT ENST00000518619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 36 publications found

Genes affected

PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

LOC157273 (HGNC:):

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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC157273	NR_040039.1	n.766-2672A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000518619.1	n.196+3429A>C		intron_variant	Intron 1 of 3	3
PPP1R3B-DT	ENST00000520255.6	n.739+3429A>C		intron_variant	Intron 2 of 3	3
PPP1R3B-DT	ENST00000520390.1	n.766-2672A>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.062
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1461729; hg19: chr8-9187242;