rs4752528

Variant names:

• chr10-121300270-A-C
• rs4752528
• ENST00000778913.1:n.177-8579T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-121300270-A-C
• chr10-121300270-A-G
• chr10-121300270-A-T

Variant summary

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

The ENST00000778913.1(ENSG00000301448):​n.177-8579T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,118 control chromosomes in the GnomAD database, including 21,678 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 (21678 hom., cov: 33)
• Consequence: ENSG00000301448 ENST00000778913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 0 publications found

Genes affected

ENSG00000301448 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378523	XR_007062320.1	n.516-8579T>G		intron_variant	Intron 1 of 1
LOC105378523	XR_007062321.1	n.515+12946T>G		intron_variant	Intron 1 of 1
LOC105378523	XR_946380.3	n.204-8579T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301448	ENST00000778913.1	n.177-8579T>G		intron_variant	Intron 2 of 2
ENSG00000301448	ENST00000778914.1	n.492-8579T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79260 AN: 152000 Hom.: 21658 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.522 AC: 79331 AN: 152118 Hom.: 21678 Cov.: 33 AF XY: 0.525 AC XY: 39023 AN XY: 74352

African (AFR) AF: 0.695 AC: 28861 AN: 41502

American (AMR) AF: 0.478 AC: 7321 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3212 AN: 5160

South Asian (SAS) AF: 0.587 AC: 2828 AN: 4816

European-Finnish (FIN) AF: 0.464 AC: 4916 AN: 10584

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29312 AN: 67966

Other (OTH) AF: 0.495 AC: 1047 AN: 2116

Alfa AF: 0.315 Hom.: 754

Bravo AF: 0.529

Asia WGS AF: 0.589 AC: 2044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4752528; hg19: chr10-123059784;