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 ENST00000441110.5(ENSG00000230333):​n.546+7294G>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 ENST00000441110.5 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441110.5. 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
	ENSG00000230333	ENST00000428533.5	TSL:5	n.138+54329G>A		intron	N/A
	ENSG00000230333	ENST00000428967.5	TSL:4	n.497+3398G>A		intron	N/A
	ENSG00000230333	ENST00000441110.5	TSL:3	n.546+7294G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs4720952;

hg19: chr7-11291400;