rs4720952

Variant names:

• chr7-11251773-G-A
• rs4720952
• ENST00000428533.5:n.138+54329G>A

Variant summary

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

The ENST00000428533.5(ENSG00000230333):​n.138+54329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,846 control chromosomes in the GnomAD database, including 25,053 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 0.57 (25053 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000428533.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 12 publications found

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230333	ENST00000428533.5	n.138+54329G>A		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.497+3398G>A		intron_variant	Intron 4 of 4	4
ENSG00000230333	ENST00000441110.5	n.546+7294G>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86549 AN: 151728 Hom.: 25018 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.571 AC: 86630 AN: 151846 Hom.: 25053 Cov.: 32 AF XY: 0.570 AC XY: 42281 AN XY: 74184

African (AFR) AF: 0.648 AC: 26833 AN: 41396

American (AMR) AF: 0.556 AC: 8475 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2327 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2805 AN: 5162

South Asian (SAS) AF: 0.493 AC: 2373 AN: 4812

European-Finnish (FIN) AF: 0.561 AC: 5895 AN: 10504

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35924 AN: 67934

Other (OTH) AF: 0.605 AC: 1278 AN: 2114

Alfa AF: 0.553 Hom.: 61392

Bravo AF: 0.577

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.5
DANN	Benign	0.66
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4720952; hg19: chr7-11291400;