chr11-69235483-G-A

Variant names:

• chr11-69235483-G-A
• rs7939250
• ENST00000779509.1:n.139-12878G>A

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-12878G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,970 control chromosomes in the GnomAD database, including 20,356 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 0.50 (20356 hom., cov: 31)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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.139-12878G>A		intron_variant	Intron 1 of 3
ENSG00000301530	ENST00000779510.1	n.76+347G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76377 AN: 151852 Hom.: 20316 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.503 AC: 76469 AN: 151970 Hom.: 20356 Cov.: 31 AF XY: 0.497 AC XY: 36892 AN XY: 74276

African (AFR) AF: 0.613 AC: 25402 AN: 41426

American (AMR) AF: 0.389 AC: 5943 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3468

East Asian (EAS) AF: 0.0600 AC: 311 AN: 5180

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4816

European-Finnish (FIN) AF: 0.469 AC: 4948 AN: 10554

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34342 AN: 67940

Other (OTH) AF: 0.527 AC: 1114 AN: 2114

Alfa AF: 0.469 Hom.: 4202

Bravo AF: 0.504

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.50
DANN	Benign	0.32
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7939250; hg19: chr11-69002950;