Menu
GeneBe

16-51137019-A-AGGGGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002968.3(SALL1):c.*92_*93insGCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0628 in 50002 control chromosomes in the gnomAD Genomes database, including 48 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.063 ( 48 hom., cov: 31)

Consequence

SALL1
NM_002968.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.456

Links

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 16-51137019-A-AGGGGC is Benign according to our data. Variant chr16-51137019-A-AGGGGC is described in ClinVar as [Benign]. Clinvar id is 1249227.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0814 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.*92_*93insGCCCC 3_prime_UTR_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.*92_*93insGCCCC 3_prime_UTR_variant 3/31 NM_002968.3 P2Q9NSC2-1
SALL1ENST00000440970.6 linkuse as main transcriptc.*92_*93insGCCCC 3_prime_UTR_variant 4/45 P2Q9NSC2-1
SALL1ENST00000685868.1 linkuse as main transcriptc.*92_*93insGCCCC 3_prime_UTR_variant 4/4 P2Q9NSC2-1
SALL1ENST00000566102.1 linkuse as main transcript downstream_gene_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0628
AC:
3141
AN:
50002
Hom.:
48
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0181
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.0892
Gnomad ASJ
AF:
0.0544
Gnomad EAS
AF:
0.00119
Gnomad SAS
AF:
0.0105
Gnomad FIN
AF:
0.0494
Gnomad MID
AF:
0.0568
Gnomad NFE
AF:
0.0864
Gnomad OTH
AF:
0.0685
GnomAD4 exome
AF:
0.0242
AC:
21374
AN:
882702
Hom.:
414
AF XY:
0.0237
AC XY:
10745
AN XY:
453942
show subpopulations
Gnomad4 AFR exome
AF:
0.00603
Gnomad4 AMR exome
AF:
0.0201
Gnomad4 ASJ exome
AF:
0.0214
Gnomad4 EAS exome
AF:
0.0000583
Gnomad4 SAS exome
AF:
0.00392
Gnomad4 FIN exome
AF:
0.0142
Gnomad4 NFE exome
AF:
0.0298
Gnomad4 OTH exome
AF:
0.0218

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 testingGeneDxMar 03, 2015- -

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: rs374006676; hg19: chr16-51170930; API