7-72951917-C-T

Variant names:

• chr7-72951917-C-T
• rs236647
• ENST00000388955.8:n.703+235G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000388955.8(NSUN5P2):​n.703+235G>A variant causes a intron 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 ENST00000388955.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 publications found

Genes affected

NSUN5P2 (HGNC:):

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000388955.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSUN5P2	NR_033323.3		n.676+235G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSUN5P2	ENST00000388955.8	TSL:1	n.703+235G>A		intron	N/A
	NSUN5P2	ENST00000444583.7	TSL:1	n.121-1721G>A		intron	N/A
	NSUN5P2	ENST00000485741.6	TSL:1	n.633+235G>A		intron	N/A

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

African (AFR) AF: 0.347 AC: 1465 AN: 4218

American (AMR) AF: 0.307 AC: 1669 AN: 5440

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 488 AN: 1818

East Asian (EAS) AF: 0.408 AC: 181 AN: 444

South Asian (SAS) AF: 0.352 AC: 591 AN: 1678

European-Finnish (FIN) AF: 0.353 AC: 1613 AN: 4570

Middle Eastern (MID) AF: 0.377 AC: 52 AN: 138

European-Non Finnish (NFE) AF: 0.378 AC: 13934 AN: 36852

Other (OTH) AF: 0.351 AC: 317 AN: 902

Alfa AF: 0.337 Hom.: 1006

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs236647;

hg19: chr7-72422456;

COSMIC: COSV57512925;