Variant chr20-51784019-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_020436.5(SALL4):c.*245dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00275 in 486,384 control chromosomes in the GnomAD database, including 8 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0041 ( 8 hom., cov: 31)

Exomes 𝑓: 0.0022 ( 0 hom. )

Consequence

SALL4
NM_020436.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

SALL4 (HGNC:15924): (spalt like transcription factor 4) This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

SALL4 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAd4 at 605 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SALL4	NM_020436.5 link	c.*245dupT	3_prime_UTR_variant	Exon 4 of 4	ENST00000217086.9	NP_065169.1	Q9UJQ4-1
SALL4	NM_001318031.2 link	c.*245dupT	3_prime_UTR_variant	Exon 4 of 4		NP_001304960.1	Q9UJQ4-2
SALL4	XM_047440318.1 link	c.*245dupT	3_prime_UTR_variant	Exon 4 of 4		XP_047296274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SALL4	ENST00000217086 link	c.*245dupT		3_prime_UTR_variant	Exon 4 of 4	1	NM_020436.5	ENSP00000217086.4		Q9UJQ4-1
SALL4	ENST00000371539.7 link	c.*245dupT		downstream_gene_variant		1		ENSP00000360594.3		Q6Y8G5

Frequencies

GnomAD3 genomes

AF:

0.00397

AC:

592

AN:

149080

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00253

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.000212

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000163

Gnomad OTH

AF:

0.00341

GnomAD4 exome

AF:

0.00217

AC:

732

AN:

337186

Hom.:

Cov.:

AF XY:

0.00188

AC XY:

339

AN XY:

180380

show subpopulations

Gnomad4 AFR exome

AF:

0.0158

Gnomad4 AMR exome

AF:

0.00209

Gnomad4 ASJ exome

AF:

0.00130

Gnomad4 EAS exome

AF:

0.00191

Gnomad4 SAS exome

AF:

0.000434

Gnomad4 FIN exome

AF:

0.00186

Gnomad4 NFE exome

AF:

0.00192

Gnomad4 OTH exome

AF:

0.00285

GnomAD4 genome

AF:

0.00406

AC:

605

AN:

149198

Hom.:

Cov.:

AF XY:

0.00409

AC XY:

297

AN XY:

72686

show subpopulations

Gnomad4 AFR

AF:

0.0131

Gnomad4 AMR

AF:

0.00253

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.000212

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000163

Gnomad4 OTH

AF:

0.00916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over