20-25540303-G-C

Variant names:

• chr20-25540303-G-C
• rs6083877
• NM_025176.6:c.-11-13705C>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.-11-13705C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,192 control chromosomes in the GnomAD database, including 4,829 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 0.22 (4829 hom., cov: 33)
• Consequence: NINL NM_025176.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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.-11-13705C>G		intron	N/A	NP_079452.3
	NINL	NM_001318226.2		c.-11-13705C>G		intron	N/A	NP_001305155.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NINL	ENST00000278886.11	TSL:1 MANE Select	c.-11-13705C>G		intron	N/A	ENSP00000278886.6
	NINL	ENST00000706725.1		n.-245C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000516514.1
	NINL	ENST00000706724.1		n.71C>G		non_coding_transcript_exon	Exon 1 of 15

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34026 AN: 152074 Hom.: 4827 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.224 AC: 34028 AN: 152192 Hom.: 4829 Cov.: 33 AF XY: 0.221 AC XY: 16441 AN XY: 74384

African (AFR) AF: 0.0571 AC: 2374 AN: 41548

American (AMR) AF: 0.252 AC: 3846 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3466

East Asian (EAS) AF: 0.00617 AC: 32 AN: 5186

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4818

European-Finnish (FIN) AF: 0.285 AC: 3014 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21360 AN: 67994

Other (OTH) AF: 0.251 AC: 530 AN: 2112

Alfa AF: 0.268 Hom.: 758

Bravo AF: 0.216

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.60
PhyloP100		0.59
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: rs6083877; hg19: chr20-25520939;