rs60718711

Variant names:

• chr20-51784019-CAAAA-C
• rs60718711
• NM_020436.5:c.*242_*245delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr20-51784019-CAAAA-C
• chr20-51784019-CAAAA-CA
• chr20-51784019-CAAAA-CAA
• chr20-51784019-CAAAA-CAAA
• chr20-51784019-CAAAA-CAAAAA
• chr20-51784019-CAAAA-CAAAAAA
• chr20-51784019-CAAAA-CAAAAAAA
• chr20-51784019-CAAAA-CAAAAAAAAAAA
• chr20-51784019-CAAAA-CAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020436.5(SALL4):​c.*242_*245delTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000671 in 149,084 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000067 (0 hom., cov: 31)
• Consequence: SALL4 NM_020436.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL4	NM_020436.5	c.*242_*245delTTTT		3_prime_UTR_variant	Exon 4 of 4	ENST00000217086.9	NP_065169.1
SALL4	NM_001318031.2	c.*242_*245delTTTT		3_prime_UTR_variant	Exon 4 of 4		NP_001304960.1
SALL4	XM_047440318.1	c.*242_*245delTTTT		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	c.*242_*245delTTTT		3_prime_UTR_variant	Exon 4 of 4	1	NM_020436.5	ENSP00000217086.4
SALL4	ENST00000371539.7	c.*242_*245delTTTT		downstream_gene_variant		1		ENSP00000360594.3

Frequencies

GnomAD3 genomes AF: 0.00000671 AC: 1 AN: 149084 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000671 AC: 1 AN: 149084 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 72560

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000149

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs60718711; hg19: chr20-50400558;