rs6083877

chr20-25540303-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NINL	NM_025176.6	c.-11-13705C>G		intron_variant		ENST00000278886.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINL	ENST00000278886.11	c.-11-13705C>G		intron_variant		1	NM_025176.6	P1
NINL	ENST00000706724.1	n.71C>G		non_coding_transcript_exon_variant	1/15
NINL	ENST00000706725.1	c.-245C>G		5_prime_UTR_variant, NMD_transcript_variant	1/15

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

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.00617

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.251

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.4
Dann	Benign	0.60

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: rs6083877; hg19: chr20-25520939;