rs8043748

Variant names:

• chr16-11752375-A-G
• rs8043748
• NM_014153.4:c.2726+294T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

TXNDC11-AS1 (HGNC:56375): (TXNDC11 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZC3H7A	NM_014153.4	c.2726+294T>C		intron_variant	Intron 22 of 22	ENST00000355758.9	NP_054872.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZC3H7A	ENST00000355758.9	c.2726+294T>C		intron_variant	Intron 22 of 22	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

African (AFR) AF: 0.855 AC: 35547 AN: 41554

American (AMR) AF: 0.658 AC: 10052 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3468

East Asian (EAS) AF: 0.848 AC: 4399 AN: 5186

South Asian (SAS) AF: 0.724 AC: 3497 AN: 4830

European-Finnish (FIN) AF: 0.487 AC: 5156 AN: 10584

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36224 AN: 67986

Other (OTH) AF: 0.618 AC: 1306 AN: 2114

Alfa AF: 0.570 Hom.: 97372

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
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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: rs8043748; hg19: chr16-11846231;