chr11-57403650-A-G

Variant names:

• chr11-57403650-A-G
• rs10792095
• ENST00000529411.1:c.303+5525T>C

Variant summary

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

The ENST00000529411.1(ENSG00000254979):​c.303+5525T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 103,998 control chromosomes in the GnomAD database, including 429 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 0.058 (429 hom., cov: 27)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0983 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.303+5525T>C		intron_variant	Intron 2 of 3	4		ENSP00000431536.1
ENSG00000254979	ENST00000528835.1	n.*212+3930T>C		intron_variant	Intron 1 of 2	3		ENSP00000431480.1
ENSG00000254979	ENST00000534081.5	n.778-4084T>C		intron_variant	Intron 7 of 12	2

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 5981 AN: 103938 Hom.: 427 Cov.: 27

Gnomad AFR AF: 0.0933

Gnomad AMI AF: 0.0562

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0287

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0140

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0576 AC: 5992 AN: 103998 Hom.: 429 Cov.: 27 AF XY: 0.0551 AC XY: 2795 AN XY: 50748

Gnomad4 AFR AF: 0.0935

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0287

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0517

Alfa AF: 0.106 Hom.: 899

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.19

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: rs10792095; hg19: chr11-57171123;