rs16987806

Positions:

• chr20-25511554-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NINL	NM_025176.6	c.451-814G>A		intron_variant		ENST00000278886.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINL	ENST00000278886.11	c.451-814G>A		intron_variant		1	NM_025176.6	P1
NINL	ENST00000706725.1	c.499-814G>A		intron_variant, NMD_transcript_variant
NINL	ENST00000706726.1	c.451-814G>A		intron_variant, NMD_transcript_variant
NINL	ENST00000706724.1	n.814-814G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.109 Hom.: 475

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

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: rs16987806; hg19: chr20-25492190;