Variant rs3841582 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_016616.5(NME8):c.528+46_528+48del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 1,454,704 control chromosomes in the GnomAD database, including 264,824 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.52 ( 21695 hom., cov: 0)

Exomes 𝑓: 0.60 ( 243129 hom. )

Consequence

NME8
NM_016616.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.287

Variant links:

Genes affected

NME8 (HGNC:16473): (NME/NM23 family member 8) This gene encodes a protein with an N-terminal thioredoxin domain and three C-terminal nucleoside diphosphate kinase (NDK) domains, but the NDK domains are thought to be catalytically inactive. The sea urchin ortholog of this gene encodes a component of sperm outer dynein arms, and the protein is implicated in ciliary function. Mutations in this gene are implicated in primary ciliary dyskinesia type 6.[provided by RefSeq, Nov 2009]

NME8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-37864463-TAAC-T is Benign according to our data. Variant chr7-37864463-TAAC-T is described in ClinVar as [Likely_benign]. Clinvar id is 260763.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NME8	NM_016616.5 linkuse as main transcript	c.528+46_528+48del		intron_variant		ENST00000199447.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
NME8	ENST00000199447.9 linkuse as main transcript	c.528+46_528+48del	intron_variant	1	NM_016616.5	P1
NME8	ENST00000440017.5 linkuse as main transcript	c.528+46_528+48del	intron_variant	1		P1
NME8	ENST00000444718.5 linkuse as main transcript	c.363+46_363+48del	intron_variant	3
NME8	ENST00000426106.1 linkuse as main transcript	c.105+7122_105+7124del	intron_variant, NMD_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78617

AN:

151546

Hom.:

21687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.606

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.639

Gnomad OTH

AF:

0.540

GnomAD3 exomes

AF:

0.548

AC:

103513

AN:

188764

Hom.:

29861

AF XY:

0.563

AC XY:

57123

AN XY:

101502

show subpopulations

Gnomad AFR exome

AF:

0.316

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.574

Gnomad EAS exome

AF:

0.351

Gnomad SAS exome

AF:

0.622

Gnomad FIN exome

AF:

0.602

Gnomad NFE exome

AF:

0.638

Gnomad OTH exome

AF:

0.569

GnomAD4 exome

AF:

0.602

AC:

784204

AN:

1303040

Hom.:

243129

AF XY:

0.604

AC XY:

391301

AN XY:

647348

show subpopulations

Gnomad4 AFR exome

AF:

0.304

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.573

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.624

Gnomad4 FIN exome

AF:

0.602

Gnomad4 NFE exome

AF:

0.628

Gnomad4 OTH exome

AF:

0.579

GnomAD4 genome

AF:

0.519

AC:

78650

AN:

151664

Hom.:

21695

Cov.:

AF XY:

0.517

AC XY:

38259

AN XY:

74066

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.462

Gnomad4 ASJ

AF:

0.581

Gnomad4 EAS

AF:

0.362

Gnomad4 SAS

AF:

0.609

Gnomad4 FIN

AF:

0.582

Gnomad4 NFE

AF:

0.639

Gnomad4 OTH

AF:

0.541

Alfa

AF:

0.586

Hom.:

4909

Bravo

AF:

0.498

Asia WGS

AF:

0.473

AC:

1643

AN:

3474

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over