chr11-130554931-A-G

Variant names:

• chr11-130554931-A-G
• rs11222164
• ENST00000777947.1:n.347+368A>G

Variant summary

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

The ENST00000777947.1(ENSG00000301321):​n.347+368A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 152,264 control chromosomes in the GnomAD database, including 774 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 0.095 (774 hom., cov: 33)
• Consequence: ENSG00000301321 ENST00000777947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 2 publications found

Genes affected

ENSG00000301321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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
ENSG00000301321	ENST00000777947.1	n.347+368A>G		intron_variant	Intron 3 of 3
ENSG00000301321	ENST00000777948.1	n.557+368A>G		intron_variant	Intron 3 of 3
ENSG00000301321	ENST00000777949.1	n.686+368A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14482 AN: 152148 Hom.: 772 Cov.: 33

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0952 AC: 14494 AN: 152264 Hom.: 774 Cov.: 33 AF XY: 0.0974 AC XY: 7248 AN XY: 74452

African (AFR) AF: 0.0643 AC: 2673 AN: 41550

American (AMR) AF: 0.0965 AC: 1477 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5176

South Asian (SAS) AF: 0.169 AC: 815 AN: 4820

European-Finnish (FIN) AF: 0.0991 AC: 1052 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6849 AN: 68016

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0999 Hom.: 1563

Bravo AF: 0.0928

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11222164; hg19: chr11-130424826;