chr20-25453185-A-C

Variant names:

• chr20-25453185-A-C
• rs12428
• NM_025176.6:c.*266T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025176.6. 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
	NINL	NM_025176.6	MANE Select	c.*266T>G		3_prime_UTR	Exon 24 of 24	NP_079452.3
	NINL	NM_001318226.2		c.*266T>G		3_prime_UTR	Exon 23 of 23	NP_001305155.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NINL	ENST00000278886.11	TSL:1 MANE Select	c.*266T>G		3_prime_UTR	Exon 24 of 24	ENSP00000278886.6
	NINL	ENST00000464285.5	TSL:2	n.1166T>G		non_coding_transcript_exon	Exon 3 of 3
	NINL	ENST00000706718.1		n.1009T>G		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.458 AC: 2571 AN: 5612

American (AMR) AF: 0.348 AC: 2059 AN: 5920

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 2086 AN: 6700

East Asian (EAS) AF: 0.913 AC: 12891 AN: 14114

South Asian (SAS) AF: 0.468 AC: 3041 AN: 6504

European-Finnish (FIN) AF: 0.432 AC: 4760 AN: 11028

Middle Eastern (MID) AF: 0.355 AC: 323 AN: 910

European-Non Finnish (NFE) AF: 0.433 AC: 48592 AN: 112322

Other (OTH) AF: 0.449 AC: 5120 AN: 11396

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

African (AFR) AF: 0.466 AC: 19321 AN: 41450

American (AMR) AF: 0.389 AC: 5943 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4763 AN: 5186

South Asian (SAS) AF: 0.477 AC: 2300 AN: 4822

European-Finnish (FIN) AF: 0.452 AC: 4768 AN: 10556

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30258 AN: 67978

Other (OTH) AF: 0.438 AC: 924 AN: 2108

Alfa AF: 0.413 Hom.: 6675

Bravo AF: 0.457

Asia WGS AF: 0.682 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.60
DANN	Benign	0.46
PhyloP100		-0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12428; hg19: chr20-25433821;