7-64356018-G-C

Variant names:

• chr7-64356018-G-C
• rs4718067
• NM_001170905.3:c.*6871G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001170905.3(ZNF736):​c.*6871G>C variant causes a 3 prime UTR 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: 32)
• Consequence: ZNF736 NM_001170905.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 publications found

Genes affected

ZNF736 (HGNC:32467): (zinc finger protein 736) Predicted to enable DNA-binding transcription factor 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TRIM60P18 (HGNC:38490): (tripartite motif containing 60 pseudogene 18)

ENSG00000287699 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF736	NM_001170905.3	c.*6871G>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000423484.3	NP_001164376.1
TRIM60P18		n.64356018G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF736	ENST00000423484.3	c.*6871G>C		3_prime_UTR_variant	Exon 4 of 4	2	NM_001170905.3	ENSP00000400852.1
TRIM60P18	ENST00000441518.1	n.647G>C		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000287699	ENST00000752301.1	n.80+15115C>G		intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1	n.50+15115C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.6
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4718067; hg19: chr7-63816396;