chr7-127651487-T-TAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000691038.2(SND1-DT):​n.363_364insTT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 41477 hom., cov: 0)

Consequence

SND1-DT
ENST00000691038.2 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.429
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SND1-DTNR_186577.1 linkuse as main transcriptn.160+185_160+186insTT intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SND1-DTENST00000691038.2 linkuse as main transcriptn.363_364insTT non_coding_transcript_exon_variant 1/1
SND1-DTENST00000490314.1 linkuse as main transcriptn.340+185_340+186insTT intron_variant 4
SND1-DTENST00000701795.1 linkuse as main transcriptn.192+185_192+186insTT intron_variant

Frequencies

GnomAD3 genomes
AF:
0.726
AC:
110124
AN:
151676
Hom.:
41431
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.917
Gnomad AMI
AF:
0.760
Gnomad AMR
AF:
0.723
Gnomad ASJ
AF:
0.786
Gnomad EAS
AF:
0.308
Gnomad SAS
AF:
0.609
Gnomad FIN
AF:
0.609
Gnomad MID
AF:
0.772
Gnomad NFE
AF:
0.665
Gnomad OTH
AF:
0.723
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.726
AC:
110224
AN:
151792
Hom.:
41477
Cov.:
0
AF XY:
0.718
AC XY:
53222
AN XY:
74154
show subpopulations
Gnomad4 AFR
AF:
0.917
Gnomad4 AMR
AF:
0.722
Gnomad4 ASJ
AF:
0.786
Gnomad4 EAS
AF:
0.308
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.609
Gnomad4 NFE
AF:
0.665
Gnomad4 OTH
AF:
0.723
Alfa
AF:
0.685
Hom.:
4486
Bravo
AF:
0.744
Asia WGS
AF:
0.509
AC:
1772
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs2308067; hg19: chr7-127291541; API