3-22990734-A-G

Variant names:

• chr3-22990734-A-G
• rs680110
• ENST00000419001.1:n.912A>G

Variant summary

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

The ENST00000419001.1(SALL4P5):​n.912A>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 0.573 in 268,250 control chromosomes in the GnomAD database, including 44,883 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 0.52 (21482 hom., cov: 34)
  • Exomes 𝑓: 0.64 (23401 hom.)
• Consequence: SALL4P5 ENST00000419001.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL4P5		n.22990734A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SALL4P5	ENST00000419001.1	n.912A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79614 AN: 151864 Hom.: 21460 Cov.: 34

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.636 AC: 73938 AN: 116268 Hom.: 23401 Cov.: 0 AF XY: 0.640 AC XY: 41121 AN XY: 64294

African (AFR) AF: 0.773 AC: 2390 AN: 3092

American (AMR) AF: 0.634 AC: 4423 AN: 6980

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 1776 AN: 2646

East Asian (EAS) AF: 0.372 AC: 901 AN: 2424

South Asian (SAS) AF: 0.640 AC: 12432 AN: 19432

European-Finnish (FIN) AF: 0.568 AC: 2955 AN: 5200

Middle Eastern (MID) AF: 0.612 AC: 256 AN: 418

European-Non Finnish (NFE) AF: 0.643 AC: 44992 AN: 69948

Other (OTH) AF: 0.622 AC: 3813 AN: 6128

GnomAD4 genome AF: 0.524 AC: 79688 AN: 151982 Hom.: 21482 Cov.: 34 AF XY: 0.519 AC XY: 38576 AN XY: 74264

African (AFR) AF: 0.603 AC: 24991 AN: 41458

American (AMR) AF: 0.536 AC: 8193 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1094 AN: 5138

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4820

European-Finnish (FIN) AF: 0.449 AC: 4730 AN: 10532

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

European-Non Finnish (NFE) AF: 0.516 AC: 35058 AN: 67954

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.519 Hom.: 64337

Bravo AF: 0.534

Asia WGS AF: 0.389 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.16
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs680110; hg19: chr3-23032225;