11-8222251-A-G

Variant names:

• chr11-8222251-A-G
• rs11041816
• ENST00000825479.1:n.229-1453A>G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000825479.1(ENSG00000307368):​n.229-1453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,112 control chromosomes in the GnomAD database, including 12,458 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 0.37 (12458 hom., cov: 32)
• Consequence: ENSG00000307368 ENST00000825479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.99
• Publications: 17 publications found

Genes affected

ENSG00000307368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825479.1. 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
	ENSG00000307368	ENST00000825479.1		n.229-1453A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55726 AN: 151994 Hom.: 12454 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.366 AC: 55723 AN: 152112 Hom.: 12458 Cov.: 32 AF XY: 0.371 AC XY: 27553 AN XY: 74360

African (AFR) AF: 0.125 AC: 5190 AN: 41508

American (AMR) AF: 0.596 AC: 9094 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3472

East Asian (EAS) AF: 0.136 AC: 707 AN: 5184

South Asian (SAS) AF: 0.415 AC: 1997 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4715 AN: 10580

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31244 AN: 67968

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.428 Hom.: 60775

Bravo AF: 0.365

Asia WGS AF: 0.260 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	19
DANN	Benign	0.83
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs11041816; hg19: chr11-8243798;