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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419001.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SALL4P5	ENST00000419001.1	TSL:6	n.912A>G		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs680110;

hg19: chr3-23032225;