rs11129411

Variant names:

• chr3-30493931-A-G
• rs11129411
• ENST00000813769.1:n.180-6662T>C

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.180-6662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,052 control chromosomes in the GnomAD database, including 25,192 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 0.56 (25192 hom., cov: 32)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 3 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 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
ENSG00000227549	ENST00000813769.1	n.180-6662T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85553 AN: 151934 Hom.: 25186 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.563 AC: 85592 AN: 152052 Hom.: 25192 Cov.: 32 AF XY: 0.568 AC XY: 42225 AN XY: 74336

African (AFR) AF: 0.374 AC: 15524 AN: 41496

American (AMR) AF: 0.568 AC: 8669 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2123 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3430 AN: 5174

South Asian (SAS) AF: 0.631 AC: 3040 AN: 4818

European-Finnish (FIN) AF: 0.687 AC: 7249 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43611 AN: 67962

Other (OTH) AF: 0.583 AC: 1227 AN: 2104

Alfa AF: 0.613 Hom.: 29924

Bravo AF: 0.545

Asia WGS AF: 0.632 AC: 2195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs11129411; hg19: chr3-30535423;