11-57394891-G-T

Variant names:

• chr11-57394891-G-T
• rs10792094
• ENST00000529411.1:c.304-4935C>A

Variant summary

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

The ENST00000529411.1(ENSG00000254979):​c.304-4935C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,034 control chromosomes in the GnomAD database, including 1,188 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 0.12 (1188 hom., cov: 31)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 8 publications found

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529411.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254979	ENST00000529411.1	TSL:4	c.304-4935C>A		intron	N/A	ENSP00000431536.1
	ENSG00000254979	ENST00000528835.1	TSL:3	n.*213-4935C>A		intron	N/A	ENSP00000431480.1
	ENSG00000254979	ENST00000534081.5	TSL:2	n.848+4605C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17955 AN: 151916 Hom.: 1188 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.118 AC: 17968 AN: 152034 Hom.: 1188 Cov.: 31 AF XY: 0.113 AC XY: 8435 AN XY: 74318

African (AFR) AF: 0.169 AC: 7026 AN: 41488

American (AMR) AF: 0.104 AC: 1593 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3468

East Asian (EAS) AF: 0.0505 AC: 260 AN: 5148

South Asian (SAS) AF: 0.0776 AC: 373 AN: 4808

European-Finnish (FIN) AF: 0.0573 AC: 606 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7470 AN: 67956

Other (OTH) AF: 0.110 AC: 232 AN: 2106

Alfa AF: 0.112 Hom.: 527

Bravo AF: 0.125

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		0.078

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

Other links and lift over

dbSNP: rs10792094; hg19: chr11-57162364;