8-14531972-A-G

Variant summary

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

The NM_139167.4(SGCZ):​c.234+22760T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,128 control chromosomes in the GnomAD database, including 4,671 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 0.22 ( 4671 hom., cov: 33)

Consequence

SGCZ
NM_139167.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.623
Variant links:
Genes affected
SGCZ (HGNC:14075): (sarcoglycan zeta) The zeta-sarcoglycan gene measures over 465 kb and localizes to 8p22. This protein is part of the sarcoglycan complex, a group of 6 proteins. The sarcoglycans are all N-glycosylated transmembrane proteins with a short intra-cellular domain, a single transmembrane region and a large extra-cellular domain containing a carboxyl-terminal cluster with several conserved cysteine residues. The sarcoglycan complex is part of the dystrophin-associated glycoprotein complex (DGC), which bridges the inner cytoskeleton and the extra-cellular matrix. [provided by RefSeq, Jul 2008]

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SGCZNM_139167.4 linkuse as main transcriptc.234+22760T>C intron_variant ENST00000382080.6
SGCZNM_001322879.2 linkuse as main transcriptc.234+22760T>C intron_variant
SGCZNM_001322880.2 linkuse as main transcriptc.234+22760T>C intron_variant
SGCZNM_001322881.2 linkuse as main transcriptc.12+22854T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SGCZENST00000382080.6 linkuse as main transcriptc.234+22760T>C intron_variant 5 NM_139167.4 P1Q96LD1-2
SGCZENST00000421524.6 linkuse as main transcriptc.195+22760T>C intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.221
AC:
33602
AN:
152010
Hom.:
4672
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0586
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.231
Gnomad ASJ
AF:
0.229
Gnomad EAS
AF:
0.107
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.313
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.319
Gnomad OTH
AF:
0.223
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.221
AC:
33617
AN:
152128
Hom.:
4671
Cov.:
33
AF XY:
0.218
AC XY:
16211
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.0585
Gnomad4 AMR
AF:
0.231
Gnomad4 ASJ
AF:
0.229
Gnomad4 EAS
AF:
0.107
Gnomad4 SAS
AF:
0.129
Gnomad4 FIN
AF:
0.313
Gnomad4 NFE
AF:
0.319
Gnomad4 OTH
AF:
0.221
Alfa
AF:
0.282
Hom.:
6004
Bravo
AF:
0.209
Asia WGS
AF:
0.117
AC:
407
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.9
DANN
Benign
0.56

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: rs1903595; hg19: chr8-14389481; API