rs16987806

Variant names:

• chr20-25511554-C-T
• rs16987806
• NM_025176.6:c.451-814G>A

Variant summary

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

The NM_025176.6(NINL):​c.451-814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,078 control chromosomes in the GnomAD database, including 1,089 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 0.11 (1089 hom., cov: 32)
• Consequence: NINL NM_025176.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NINL	NM_025176.6	c.451-814G>A		intron_variant	Intron 4 of 23	ENST00000278886.11	NP_079452.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NINL	ENST00000278886.11	c.451-814G>A		intron_variant	Intron 4 of 23	1	NM_025176.6	ENSP00000278886.6
NINL	ENST00000706724.1	n.814-814G>A		intron_variant	Intron 4 of 14
NINL	ENST00000706725.1	n.499-814G>A		intron_variant	Intron 4 of 14			ENSP00000516514.1
NINL	ENST00000706726.1	n.451-814G>A		intron_variant	Intron 4 of 17			ENSP00000516515.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17230 AN: 151960 Hom.: 1087 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0963

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17240 AN: 152078 Hom.: 1089 Cov.: 32 AF XY: 0.112 AC XY: 8291 AN XY: 74324

African (AFR) AF: 0.155 AC: 6442 AN: 41468

American (AMR) AF: 0.0663 AC: 1014 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0965 AC: 464 AN: 4808

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10566

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7323 AN: 67990

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.108 Hom.: 523

Bravo AF: 0.110

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.81
PhyloP100		-1.6
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: rs16987806; hg19: chr20-25492190;