rs8043748

Positions:

• chr16-11752375-A-G

Variant summary

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

The NM_014153.4(ZC3H7A):​c.2726+294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,206 control chromosomes in the GnomAD database, including 33,717 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 0.65 (33717 hom., cov: 33)
• Consequence: ZC3H7A NM_014153.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

ZC3H7A (HGNC:30959): (zinc finger CCCH-type containing 7A) Enables miRNA binding activity. Involved in production of miRNAs involved in gene silencing by miRNA. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZC3H7A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H7A	NM_014153.4	c.2726+294T>C		intron_variant		ENST00000355758.9	NP_054872.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZC3H7A	ENST00000355758.9	c.2726+294T>C		intron_variant		1	NM_014153.4	ENSP00000347999.4

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98489 AN: 152088 Hom.: 33663 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.648 AC: 98601 AN: 152206 Hom.: 33717 Cov.: 33 AF XY: 0.650 AC XY: 48364 AN XY: 74412

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.618

Alfa AF: 0.552 Hom.: 39434

Bravo AF: 0.668

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.079
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs8043748; hg19: chr16-11846231;