rs6625978

Positions:

• chrX-72198819-C-A
• chrX-72198819-C-G

Variant summary

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

The ENST00000498736.3(RN7SL388P):​n.108C>A 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 0.424 in 109,338 control chromosomes in the GnomAD database, including 8,964 homozygotes. There are 13,324 hemizygotes in GnomAD. 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 0.42 (8964 hom., 13316 hem., cov: 21)
  • Exomes 𝑓: 0.22 (0 hom. 8 hem.)
• Consequence: RN7SL388P ENST00000498736.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

RN7SL388P (HGNC:46404): (RNA, 7SL, cytoplasmic 388, pseudogene)

PIN4 (HGNC:8992): (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) This gene encodes a member of the parvulin subfamily of the peptidyl-prolyl cis/trans isomerase protein family. The encoded protein catalyzes the isomerization of peptidylprolyl bonds, and may play a role in the cell cycle, chromatin remodeling, and/or ribosome biogenesis. The encoded protein may play an additional role in the mitochondria. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIN4	NM_001170747.1	c.312+1915C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RN7SL388P	ENST00000498736.3	n.108C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 46341 AN: 109237 Hom.: 8966 Cov.: 21 AF XY: 0.421 AC XY: 13280 AN XY: 31581

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.380

GnomAD4 exome AF: 0.216 AC: 11 AN: 51 Hom.: 0 Cov.: 0 AF XY: 0.421 AC XY: 8 AN XY: 19

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.424 AC: 46382 AN: 109287 Hom.: 8964 Cov.: 21 AF XY: 0.421 AC XY: 13316 AN XY: 31641

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.385

Alfa AF: 0.343 Hom.: 2337

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6625978; hg19: chrX-71418669;