11-57399188-T-C

Variant names:

• chr11-57399188-T-C
• rs3851114
• ENST00000529411.1:c.304-9232A>G

Variant summary

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

The ENST00000529411.1(ENSG00000254979):​c.304-9232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,112 control chromosomes in the GnomAD database, including 22,869 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 0.53 (22869 hom., cov: 33)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 6 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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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

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
	ENSG00000254979	ENST00000529411.1	TSL:4	c.304-9232A>G		intron	N/A	ENSP00000431536.1	H0YCG3
	ENSG00000254979	ENST00000528835.1	TSL:3	n.*212+8392A>G		intron	N/A	ENSP00000431480.1	H0YCF1
	ENSG00000254979	ENST00000534081.5	TSL:2	n.848+308A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80136 AN: 151994 Hom.: 22856 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.527 AC: 80169 AN: 152112 Hom.: 22869 Cov.: 33 AF XY: 0.540 AC XY: 40128 AN XY: 74364

African (AFR) AF: 0.297 AC: 12332 AN: 41478

American (AMR) AF: 0.679 AC: 10373 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3839 AN: 5184

South Asian (SAS) AF: 0.740 AC: 3568 AN: 4820

European-Finnish (FIN) AF: 0.684 AC: 7238 AN: 10582

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38774 AN: 67988

Other (OTH) AF: 0.540 AC: 1139 AN: 2108

Alfa AF: 0.558 Hom.: 73422

Bravo AF: 0.517

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	9.0
DANN	Benign	0.91
PhyloP100		0.31

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

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

Other links and lift over

dbSNP: rs3851114;

hg19: chr11-57166661;