chr11-69206503-A-G

Variant names:

• chr11-69206503-A-G
• rs4255548
• ENST00000779509.1:n.138+10321A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+10321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 150,090 control chromosomes in the GnomAD database, including 29,757 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 0.63 (29757 hom., cov: 27)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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
ENSG00000301530	ENST00000779509.1	n.138+10321A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.628 AC: 94124 AN: 149974 Hom.: 29725 Cov.: 27

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.628 AC: 94209 AN: 150090 Hom.: 29757 Cov.: 27 AF XY: 0.630 AC XY: 46072 AN XY: 73188

African (AFR) AF: 0.682 AC: 27772 AN: 40728

American (AMR) AF: 0.543 AC: 8198 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2541 AN: 3456

East Asian (EAS) AF: 0.465 AC: 2336 AN: 5022

South Asian (SAS) AF: 0.547 AC: 2583 AN: 4720

European-Finnish (FIN) AF: 0.671 AC: 6892 AN: 10268

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.620 AC: 41884 AN: 67540

Other (OTH) AF: 0.642 AC: 1336 AN: 2082

Alfa AF: 0.620 Hom.: 109516

Bravo AF: 0.622

Asia WGS AF: 0.568 AC: 1916 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs4255548; hg19: chr11-68973970;