11-69208652-T-C

Variant names:

• chr11-69208652-T-C
• rs4495900
• ENST00000779509.1:n.138+12470T>C

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+12470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,054 control chromosomes in the GnomAD database, including 32,648 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 0.65 (32648 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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+12470T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98723 AN: 151936 Hom.: 32611 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.650 AC: 98816 AN: 152054 Hom.: 32648 Cov.: 32 AF XY: 0.649 AC XY: 48276 AN XY: 74332

African (AFR) AF: 0.762 AC: 31605 AN: 41480

American (AMR) AF: 0.548 AC: 8370 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2551 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2373 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2630 AN: 4814

European-Finnish (FIN) AF: 0.667 AC: 7051 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42166 AN: 67962

Other (OTH) AF: 0.661 AC: 1399 AN: 2116

Alfa AF: 0.616 Hom.: 5734

Bravo AF: 0.649

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.095
DANN	Benign	0.19
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs4495900; hg19: chr11-68976119;