chr14-68792785-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439696.3(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. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.24 (5049 hom., cov: 31)
  • Exomes 𝑓: 0.21 (31103 hom.)
• Consequence: ZFP36L1 ENST00000439696.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 22 publications found

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439696.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP36L1	NM_004926.4	MANE Select	c.57+97A>G		intron	N/A	NP_004917.2
	ZFP36L1	NM_001244701.1		c.264+97A>G		intron	N/A	NP_001231630.1
	ZFP36L1	NM_001244698.2		c.57+97A>G		intron	N/A	NP_001231627.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP36L1	ENST00000439696.3	TSL:1 MANE Select	c.57+97A>G		intron	N/A	ENSP00000388402.2
	ZFP36L1	ENST00000336440.5	TSL:2	c.57+97A>G		intron	N/A	ENSP00000337386.3
	ZFP36L1	ENST00000557086.1	TSL:2	c.76-2293A>G		intron	N/A	ENSP00000450784.1

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

African (AFR) AF: 0.356 AC: 11132 AN: 31240

American (AMR) AF: 0.120 AC: 5298 AN: 44226

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 6010 AN: 25238

East Asian (EAS) AF: 0.00870 AC: 338 AN: 38852

South Asian (SAS) AF: 0.204 AC: 17151 AN: 83986

European-Finnish (FIN) AF: 0.184 AC: 9334 AN: 50858

Middle Eastern (MID) AF: 0.218 AC: 1095 AN: 5016

European-Non Finnish (NFE) AF: 0.215 AC: 221591 AN: 1031172

Other (OTH) 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

African (AFR) AF: 0.352 AC: 14597 AN: 41504

American (AMR) AF: 0.182 AC: 2790 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3470

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5186

South Asian (SAS) AF: 0.191 AC: 920 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1840 AN: 10608

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15063 AN: 67998

Other (OTH) AF: 0.221 AC: 467 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		-0.67
PromoterAI		0.037	Neutral
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: rs11851414; hg19: chr14-69259502;