rs6828740

chr4-117413463-T-C

Variant summary

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

The ENST00000413753.1(RPSAP35):n.2T>C 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 0.056 in 152,114 control chromosomes in the GnomAD database, including 378 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 0.056 (378 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPSAP35 ENST00000413753.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

RPSAP35 (HGNC:36447): (ribosomal protein SA pseudogene 35)

LINC01378 (HGNC:50645): (long intergenic non-protein coding RNA 1378)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPSAP35	ENST00000413753.1	n.2T>C		non_coding_transcript_exon_variant	1/1
LINC01378	ENST00000626258.2	n.200+7098T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8506 AN: 151996 Hom.: 377 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0492

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0560 AC: 8520 AN: 152114 Hom.: 378 Cov.: 32 AF XY: 0.0537 AC XY: 3993 AN XY: 74380

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0357

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0512 Hom.: 32

Bravo AF: 0.0614

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6828740; hg19: chr4-118334619;