6-7920671-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_037616.1(BLOC1S5-TXNDC5):​n.423-15948T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,948 control chromosomes in the GnomAD database, including 19,326 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 0.49 ( 19326 hom., cov: 32)

Consequence

BLOC1S5-TXNDC5
NR_037616.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00100
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BLOC1S5-TXNDC5NR_037616.1 linkuse as main transcriptn.423-15948T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.494
AC:
74932
AN:
151830
Hom.:
19297
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.641
Gnomad AMI
AF:
0.369
Gnomad AMR
AF:
0.485
Gnomad ASJ
AF:
0.332
Gnomad EAS
AF:
0.438
Gnomad SAS
AF:
0.608
Gnomad FIN
AF:
0.431
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.450
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.494
AC:
75019
AN:
151948
Hom.:
19326
Cov.:
32
AF XY:
0.498
AC XY:
36947
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.641
Gnomad4 AMR
AF:
0.486
Gnomad4 ASJ
AF:
0.332
Gnomad4 EAS
AF:
0.438
Gnomad4 SAS
AF:
0.608
Gnomad4 FIN
AF:
0.431
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.421
Hom.:
29491
Bravo
AF:
0.495
Asia WGS
AF:
0.532
AC:
1851
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.87
DANN
Benign
0.43

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: rs365936; hg19: chr6-7920904; API