rs12428

Positions:

• chr20-25453185-A-C
• chr20-25453185-A-T

Variant summary

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

The NM_025176.6(NINL):​c.*266T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 326,544 control chromosomes in the GnomAD database, including 37,754 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 0.46 (16709 hom., cov: 32)
  • Exomes 𝑓: 0.47 (21045 hom.)
• Consequence: NINL NM_025176.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

NINL (HGNC:29163): (ninein like) Predicted to enable calcium ion binding activity. Predicted to be involved in microtubule anchoring at centrosome. Located in cytosol; intercellular bridge; and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

NINL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NINL	NM_025176.6	c.*266T>G		3_prime_UTR_variant	24/24	ENST00000278886.11	NP_079452.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NINL	ENST00000278886	c.*266T>G		3_prime_UTR_variant	24/24	1	NM_025176.6	ENSP00000278886.6

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69945 AN: 151920 Hom.: 16699 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.467 AC: 81443 AN: 174506 Hom.: 21045 Cov.: 3 AF XY: 0.466 AC XY: 41475 AN XY: 89042

Gnomad4 AFR exome AF: 0.458

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.311

Gnomad4 EAS exome AF: 0.913

Gnomad4 SAS exome AF: 0.468

Gnomad4 FIN exome AF: 0.432

Gnomad4 NFE exome AF: 0.433

Gnomad4 OTH exome AF: 0.449

GnomAD4 genome AF: 0.460 AC: 69988 AN: 152038 Hom.: 16709 Cov.: 32 AF XY: 0.461 AC XY: 34283 AN XY: 74326

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.438

Alfa AF: 0.407 Hom.: 5500

Bravo AF: 0.457

Asia WGS AF: 0.682 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.60
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12428; hg19: chr20-25433821;