chr11-69196811-C-T

Variant names:

• chr11-69196811-C-T
• rs11228554
• ENST00000779509.1:n.138+629C>T

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,110 control chromosomes in the GnomAD database, including 17,378 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 0.44 (17378 hom., cov: 33)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 2 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779509.1. 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
	ENSG00000301530	ENST00000779509.1		n.138+629C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67338 AN: 151992 Hom.: 17336 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.443 AC: 67440 AN: 152110 Hom.: 17378 Cov.: 33 AF XY: 0.443 AC XY: 32945 AN XY: 74360

African (AFR) AF: 0.724 AC: 30072 AN: 41508

American (AMR) AF: 0.381 AC: 5824 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2013 AN: 5152

South Asian (SAS) AF: 0.375 AC: 1810 AN: 4828

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10580

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21223 AN: 67962

Other (OTH) AF: 0.409 AC: 864 AN: 2114

Alfa AF: 0.361 Hom.: 29642

Bravo AF: 0.461

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.51
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11228554; hg19: chr11-68964278;