ENST00000419001.1:n.1027A>G

Variant names:

• chr3-22990849-A-G
• rs497387
• ENST00000419001.1:n.1027A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419001.1(SALL4P5):​n.1027A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 169,924 control chromosomes in the GnomAD database, including 27,125 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 0.53 (22105 hom., cov: 35)
  • Exomes 𝑓: 0.76 (5020 hom.)
• Consequence: SALL4P5 ENST00000419001.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 1 publications found

Genes affected

SALL4P5 (HGNC:39822): (spalt like transcription factor 4 pseudogene 5)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL4P5		n.22990849A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SALL4P5	ENST00000419001.1	n.1027A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81155 AN: 152088 Hom.: 22079 Cov.: 35

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.524

GnomAD4 exome AF: 0.763 AC: 13519 AN: 17716 Hom.: 5020 Cov.: 0 AF XY: 0.760 AC XY: 6956 AN XY: 9148

African (AFR) AF: 0.836 AC: 286 AN: 342

American (AMR) AF: 0.791 AC: 478 AN: 604

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 269 AN: 378

East Asian (EAS) AF: 0.640 AC: 64 AN: 100

South Asian (SAS) AF: 0.773 AC: 1686 AN: 2180

European-Finnish (FIN) AF: 0.744 AC: 519 AN: 698

Middle Eastern (MID) AF: 0.797 AC: 51 AN: 64

European-Non Finnish (NFE) AF: 0.762 AC: 9293 AN: 12192

Other (OTH) AF: 0.754 AC: 873 AN: 1158

GnomAD4 genome AF: 0.534 AC: 81225 AN: 152208 Hom.: 22105 Cov.: 35 AF XY: 0.530 AC XY: 39429 AN XY: 74420

African (AFR) AF: 0.604 AC: 25091 AN: 41548

American (AMR) AF: 0.529 AC: 8093 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1402 AN: 5170

South Asian (SAS) AF: 0.469 AC: 2267 AN: 4832

European-Finnish (FIN) AF: 0.509 AC: 5393 AN: 10588

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35566 AN: 67990

Other (OTH) AF: 0.524 AC: 1108 AN: 2114

Alfa AF: 0.523 Hom.: 17467

Bravo AF: 0.541

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.077
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs497387; hg19: chr3-23032340;