chr7-72951917-C-T

Position:

• chr7-72951917-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_033323.3(NSUN5P2):​n.676+235G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.36 (7469 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: NSUN5P2 NR_033323.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

NSUN5P2 (HGNC:16609): (NSUN5 pseudogene 2) This locus represents a transcribed pseudogene of a nearby locus on chromosome 7, which encodes a putative methyltransferase. There is also a third closely related pseudogene locus in this region. There is extensive alternative splicing at this locus. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSUN5P2	NR_033323.3	n.676+235G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSUN5P2	ENST00000457352.4	n.486+1409G>A		intron_variant, non_coding_transcript_variant
NSUN5P2	ENST00000602348.5	n.83-1721G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 20522 AN: 56498 Hom.: 7457 Cov.: 0

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.338

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.364 AC: 20546 AN: 56506 Hom.: 7469 Cov.: 0 AF XY: 0.361 AC XY: 9650 AN XY: 26746

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.351

Alfa AF: 0.337 Hom.: 1006

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs236647; hg19: chr7-72422456; COSMIC: COSV57512925;