5-180849584-C-T

Variant names:

• chr5-180849584-C-T
• rs138541087
• NM_001172638.2:c.1911G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001172638.2(ZFP62):​c.1911G>A​(p.Arg637Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ZFP62 NM_001172638.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 0 publications found

Genes affected

ZFP62 (HGNC:23241): (ZFP62 zinc finger protein) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

HEIH (HGNC:45049): (hepatocellular carcinoma up-regulated EZH2-associated long non-coding RNA)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP7: Synonymous conserved (PhyloP=-1.73 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172638.2. 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
	ZFP62	NM_001172638.2	MANE Select	c.1911G>A	p.Arg637Arg	synonymous	Exon 2 of 2	NP_001166109.1	Q8NB50-1
	ZFP62	NM_001377943.1		c.1911G>A	p.Arg637Arg	synonymous	Exon 2 of 2	NP_001364872.1	Q8NB50-1
	ZFP62	NM_001377939.1		c.1812G>A	p.Arg604Arg	synonymous	Exon 4 of 4	NP_001364868.1	Q8NB50-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP62	ENST00000502412.2	TSL:2 MANE Select	c.1911G>A	p.Arg637Arg	synonymous	Exon 2 of 2	ENSP00000423820.1	Q8NB50-1
	ZFP62	ENST00000506377.5	TSL:1	n.254-1502G>A		intron	N/A
	ZFP62	ENST00000512132.5	TSL:2	c.1812G>A	p.Arg604Arg	synonymous	Exon 3 of 3	ENSP00000426193.1	Q8NB50-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 78

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.4
DANN	Benign	0.50
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs138541087; hg19: chr5-180276584;