chr7-37850184-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016616.5(NME8):​c.-7-76A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 1,110,362 control chromosomes in the GnomAD database, including 103,026 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 11094 hom., cov: 32)
Exomes 𝑓: 0.43 ( 91932 hom. )

Consequence

NME8
NM_016616.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.04
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 7-37850184-A-G is Benign according to our data. Variant chr7-37850184-A-G is described in ClinVar as [Benign]. Clinvar id is 1248020.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NME8NM_016616.5 linkuse as main transcriptc.-7-76A>G intron_variant ENST00000199447.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NME8ENST00000199447.9 linkuse as main transcriptc.-7-76A>G intron_variant 1 NM_016616.5 P1
NME8ENST00000440017.5 linkuse as main transcriptc.-7-76A>G intron_variant 1 P1
NME8ENST00000444718.5 linkuse as main transcriptc.-7-76A>G intron_variant 3
NME8ENST00000455500.5 linkuse as main transcriptc.-7-76A>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.356
AC:
54062
AN:
151986
Hom.:
11095
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.138
Gnomad AMI
AF:
0.613
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.463
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.433
Gnomad FIN
AF:
0.446
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.461
Gnomad OTH
AF:
0.383
GnomAD4 exome
AF:
0.432
AC:
413802
AN:
958256
Hom.:
91932
AF XY:
0.434
AC XY:
216685
AN XY:
498804
show subpopulations
Gnomad4 AFR exome
AF:
0.128
Gnomad4 AMR exome
AF:
0.313
Gnomad4 ASJ exome
AF:
0.454
Gnomad4 EAS exome
AF:
0.368
Gnomad4 SAS exome
AF:
0.435
Gnomad4 FIN exome
AF:
0.477
Gnomad4 NFE exome
AF:
0.450
Gnomad4 OTH exome
AF:
0.423
GnomAD4 genome
AF:
0.355
AC:
54065
AN:
152106
Hom.:
11094
Cov.:
32
AF XY:
0.358
AC XY:
26593
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.137
Gnomad4 AMR
AF:
0.348
Gnomad4 ASJ
AF:
0.463
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.435
Gnomad4 FIN
AF:
0.446
Gnomad4 NFE
AF:
0.461
Gnomad4 OTH
AF:
0.384
Alfa
AF:
0.414
Hom.:
1788
Bravo
AF:
0.336
Asia WGS
AF:
0.352
AC:
1219
AN:
3470

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
7.2
DANN
Benign
0.93

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.

Other links and lift over

dbSNP: rs10271309; hg19: chr7-37889786; API