rs11851414

chr14-68792785-T-Cchr14-68792785-T-G

Variant summary

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

The NM_004926.4(ZFP36L1):c.57+97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,519,730 control chromosomes in the GnomAD database, including 36,152 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 0.24 (5049 hom., cov: 31)
  • Exomes 𝑓: 0.21 (31103 hom.)
• Consequence: ZFP36L1 NM_004926.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

Genes affected

ZFP36L1 (HGNC:1107): (ZFP36 ring finger protein like 1) This gene is a member of the TIS11 family of early response genes, which are induced by various agonists such as the phorbol ester TPA and the polypeptide mitogen EGF. This gene is well conserved across species and has a promoter that contains motifs seen in other early-response genes. The encoded protein contains a distinguishing putative zinc finger domain with a repeating cys-his motif. This putative nuclear transcription factor most likely functions in regulating the response to growth factors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFP36L1	NM_004926.4	c.57+97A>G		intron_variant		ENST00000439696.3
ZFP36L1	NM_001244698.2	c.57+97A>G		intron_variant
ZFP36L1	NM_001244701.1	c.264+97A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFP36L1	ENST00000439696.3	c.57+97A>G		intron_variant		1	NM_004926.4	P1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36868 AN: 152066 Hom.: 5054 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.207 AC: 283685 AN: 1367546 Hom.: 31103 AF XY: 0.208 AC XY: 142496 AN XY: 685200

Gnomad4 AFR exome AF: 0.356

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.238

Gnomad4 EAS exome AF: 0.00870

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.242 AC: 36891 AN: 152184 Hom.: 5049 Cov.: 31 AF XY: 0.236 AC XY: 17524 AN XY: 74408

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.00694

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.221

Alfa AF: 0.217 Hom.: 5180

Bravo AF: 0.247

Asia WGS AF: 0.108 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.9
Dann	Benign	0.61

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: rs11851414; hg19: chr14-69259502;