rs4718142

Positions:

• chr7-64846442-T-C

Variant summary

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

The NR_073389.2(ZNF138):​n.272-5357T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,024 control chromosomes in the GnomAD database, including 14,139 homozygotes. 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 0.43 (14139 hom., cov: 32)
• Consequence: ZNF138 NR_073389.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

ZNF138 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF138	NR_073389.2	n.272-5357T>C		intron_variant, non_coding_transcript_variant
ZNF138	NR_160268.1	n.145-5357T>C		intron_variant, non_coding_transcript_variant
ZNF138	NR_160269.1	n.272-5357T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64993 AN: 151906 Hom.: 14138 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.428 AC: 65010 AN: 152024 Hom.: 14139 Cov.: 32 AF XY: 0.427 AC XY: 31733 AN XY: 74298

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.412

Alfa AF: 0.442 Hom.: 1854

Bravo AF: 0.426

Asia WGS AF: 0.295 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4718142; hg19: chr7-64306820;