rs11851414

Variant names:

• chr14-68792785-T-C
• rs11851414
• NM_004926.4:c.57+97A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-68792785-T-C
• chr14-68792785-T-G

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZFP36L1	NM_004926.4	c.57+97A>G		intron_variant	Intron 1 of 1	ENST00000439696.3	NP_004917.2
ZFP36L1	NM_001244701.1	c.264+97A>G		intron_variant	Intron 2 of 2		NP_001231630.1
ZFP36L1	NM_001244698.2	c.57+97A>G		intron_variant	Intron 1 of 2		NP_001231627.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP36L1	ENST00000439696.3	c.57+97A>G		intron_variant	Intron 1 of 1	1	NM_004926.4	ENSP00000388402.2

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 AC: 11132 AN: 31240

Gnomad4 AMR exome AF: 0.120 AC: 5298 AN: 44226

Gnomad4 ASJ exome AF: 0.238 AC: 6010 AN: 25238

Gnomad4 EAS exome AF: 0.00870 AC: 338 AN: 38852

Gnomad4 SAS exome AF: 0.204 AC: 17151 AN: 83986

Gnomad4 FIN exome AF: 0.184 AC: 9334 AN: 50858

Gnomad4 NFE exome AF: 0.215 AC: 221591 AN: 1031172

Gnomad4 Remaining exome AF: 0.206 AC: 11736 AN: 56958

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 AC: 0.351701 AN: 0.351701

Gnomad4 AMR AF: 0.182 AC: 0.182496 AN: 0.182496

Gnomad4 ASJ AF: 0.248 AC: 0.248127 AN: 0.248127

Gnomad4 EAS AF: 0.00694 AC: 0.00694177 AN: 0.00694177

Gnomad4 SAS AF: 0.191 AC: 0.19103 AN: 0.19103

Gnomad4 FIN AF: 0.173 AC: 0.173454 AN: 0.173454

Gnomad4 NFE AF: 0.222 AC: 0.221521 AN: 0.221521

Gnomad4 OTH AF: 0.221 AC: 0.221327 AN: 0.221327

Alfa AF: 0.222 Hom.: 6777

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs11851414; hg19: chr14-69259502;