rs755523

Variant names:

• chr4-52823764-A-G
• rs755523
• ENST00000650700.1:n.988+7210A>G

Variant summary

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

The ENST00000650700.1(ENSG00000293643):​n.988+7210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,278 control chromosomes in the GnomAD database, including 643 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 0.064 (643 hom., cov: 32)
• Consequence: ENSG00000293643 ENST00000650700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 2 publications found

Genes affected

ENSG00000293643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650700.1. 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
	ENSG00000293643	ENST00000650700.1		n.988+7210A>G		intron	N/A
	ENSG00000293643	ENST00000652441.1		n.504-39504A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9680 AN: 152160 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0636 AC: 9688 AN: 152278 Hom.: 643 Cov.: 32 AF XY: 0.0633 AC XY: 4711 AN XY: 74460

African (AFR) AF: 0.167 AC: 6923 AN: 41528

American (AMR) AF: 0.0244 AC: 373 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5176

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4828

European-Finnish (FIN) AF: 0.0315 AC: 335 AN: 10624

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0239 AC: 1623 AN: 68024

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0581 Hom.: 72

Bravo AF: 0.0679

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.77
PhyloP100		-0.23

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: rs755523;

hg19: chr4-53689931;