X-71941232-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001013627.3(NHSL2):​c.280+29865C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.71 ( 22089 hom., 22921 hem., cov: 22)
Failed GnomAD Quality Control

Consequence

NHSL2
NM_001013627.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980
Variant links:
Genes affected
NHSL2 (HGNC:33737): (NHS like 2) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NHSL2NM_001013627.3 linkc.280+29865C>G intron_variant Intron 1 of 7 ENST00000633930.2 NP_001013649.2 Q5HYW2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NHSL2ENST00000633930.2 linkc.280+29865C>G intron_variant Intron 1 of 7 5 NM_001013627.3 ENSP00000488668.1 Q5HYW2-1

Frequencies

GnomAD3 genomes
AF:
0.706
AC:
77680
AN:
110018
Hom.:
22091
Cov.:
22
AF XY:
0.710
AC XY:
22896
AN XY:
32234
show subpopulations
Gnomad AFR
AF:
0.296
Gnomad AMI
AF:
0.916
Gnomad AMR
AF:
0.759
Gnomad ASJ
AF:
0.956
Gnomad EAS
AF:
0.597
Gnomad SAS
AF:
0.771
Gnomad FIN
AF:
0.899
Gnomad MID
AF:
0.877
Gnomad NFE
AF:
0.896
Gnomad OTH
AF:
0.761
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.706
AC:
77694
AN:
110074
Hom.:
22089
Cov.:
22
AF XY:
0.710
AC XY:
22921
AN XY:
32300
show subpopulations
Gnomad4 AFR
AF:
0.296
Gnomad4 AMR
AF:
0.759
Gnomad4 ASJ
AF:
0.956
Gnomad4 EAS
AF:
0.599
Gnomad4 SAS
AF:
0.772
Gnomad4 FIN
AF:
0.899
Gnomad4 NFE
AF:
0.896
Gnomad4 OTH
AF:
0.766
Alfa
AF:
0.663
Hom.:
2857
Bravo
AF:
0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.84
DANN
Benign
0.41

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: rs7471388; hg19: chrX-71161082; API