chr11-69210034-G-A

Variant names:

• chr11-69210034-G-A
• rs12281017
• ENST00000779509.1:n.138+13852G>A

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+13852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,244 control chromosomes in the GnomAD database, including 2,270 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 0.16 (2270 hom., cov: 33)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 9 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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+13852G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24645 AN: 152126 Hom.: 2271 Cov.: 33

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.162 AC: 24630 AN: 152244 Hom.: 2270 Cov.: 33 AF XY: 0.160 AC XY: 11918 AN XY: 74438

African (AFR) AF: 0.0895 AC: 3720 AN: 41554

American (AMR) AF: 0.144 AC: 2198 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3464

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5178

South Asian (SAS) AF: 0.195 AC: 942 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1596 AN: 10616

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14336 AN: 67990

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.198 Hom.: 3739

Bravo AF: 0.157

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.54
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12281017; hg19: chr11-68977501;