chr11-69197107-C-G

Variant names:

• chr11-69197107-C-G
• rs11602052
• ENST00000779509.1:n.138+925C>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+925C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 142,866 control chromosomes in the GnomAD database, including 18,400 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 0.52 (18400 hom., cov: 31)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 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+925C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 74054 AN: 142746 Hom.: 18382 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.519 AC: 74120 AN: 142866 Hom.: 18400 Cov.: 31 AF XY: 0.524 AC XY: 36559 AN XY: 69734

African (AFR) AF: 0.570 AC: 22717 AN: 39848

American (AMR) AF: 0.582 AC: 8345 AN: 14336

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1220 AN: 3222

East Asian (EAS) AF: 0.516 AC: 2326 AN: 4508

South Asian (SAS) AF: 0.673 AC: 3075 AN: 4570

European-Finnish (FIN) AF: 0.500 AC: 4823 AN: 9654

Middle Eastern (MID) AF: 0.433 AC: 116 AN: 268

European-Non Finnish (NFE) AF: 0.473 AC: 30140 AN: 63664

Other (OTH) AF: 0.475 AC: 943 AN: 1986

Alfa AF: 0.465 Hom.: 1737

Asia WGS AF: 0.529 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11602052; hg19: chr11-68964574; COSMIC: COSV65757743;