rs526572

Variant names:

• chr11-57394409-T-A
• rs526572
• ENST00000529411.1:c.304-4453A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-57394409-T-A
• chr11-57394409-T-C
• chr11-57394409-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000529411.1(ENSG00000254979):​c.304-4453A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,084 control chromosomes in the GnomAD database, including 39,577 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 0.72 (39577 hom., cov: 32)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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
ENSG00000254979	ENST00000529411.1	c.304-4453A>T		intron_variant	Intron 2 of 3	4		ENSP00000431536.1
ENSG00000254979	ENST00000528835.1	n.*213-4453A>T		intron_variant	Intron 1 of 2	3		ENSP00000431480.1
ENSG00000254979	ENST00000534081.5	n.849-4453A>T		intron_variant	Intron 8 of 12	2

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109210 AN: 151966 Hom.: 39563 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.719 AC: 109276 AN: 152084 Hom.: 39577 Cov.: 32 AF XY: 0.723 AC XY: 53766 AN XY: 74356

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.726

Alfa AF: 0.654 Hom.: 1950

Bravo AF: 0.720

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs526572; hg19: chr11-57161882;