rs4841132

chr8-9326086-A-Gchr8-9326086-A-T

Variant summary

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

The NR_040039.1(LOC157273):n.548A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,496 control chromosomes in the GnomAD database, including 61,117 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 0.89 (61030 hom., cov: 34)
  • Exomes 𝑓: 0.95 (87 hom.)
• Consequence: LOC157273 NR_040039.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

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

LOC157273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC157273	NR_040039.1	n.548A>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R3B-DT	ENST00000523246.2	n.784A>G		non_coding_transcript_exon_variant	3/6	5

Frequencies

GnomAD3 genomes AF: 0.894 AC: 136085 AN: 152186 Hom.: 60999 Cov.: 34

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.893

GnomAD4 exome AF: 0.948 AC: 182 AN: 192 Hom.: 87 Cov.: 0 AF XY: 0.954 AC XY: 124 AN XY: 130

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.958

Gnomad4 NFE exome AF: 0.939

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.894 AC: 136174 AN: 152304 Hom.: 61030 Cov.: 34 AF XY: 0.890 AC XY: 66288 AN XY: 74468

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.888

Alfa AF: 0.917 Hom.: 73766

Bravo AF: 0.891

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.15
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4841132; hg19: chr8-9183596;