11-63016300-A-G

Variant names:

• chr11-63016300-A-G
• rs3809069
• ENST00000782248.1:n.847-9605A>G

Variant summary

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

The ENST00000782248.1(ENSG00000301851):​n.847-9605A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,166 control chromosomes in the GnomAD database, including 1,846 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 0.14 (1846 hom., cov: 32)
• Consequence: ENSG00000301851 ENST00000782248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 5 publications found

Genes affected

ENSG00000301851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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
ENSG00000301851	ENST00000782248.1	n.847-9605A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20712 AN: 152048 Hom.: 1841 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.136 AC: 20710 AN: 152166 Hom.: 1846 Cov.: 32 AF XY: 0.139 AC XY: 10327 AN XY: 74384

African (AFR) AF: 0.0362 AC: 1504 AN: 41560

American (AMR) AF: 0.123 AC: 1877 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1522 AN: 5158

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1814 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11209 AN: 67952

Other (OTH) AF: 0.148 AC: 311 AN: 2106

Alfa AF: 0.150 Hom.: 3682

Bravo AF: 0.127

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.3
PromoterAI		0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3809069; hg19: chr11-62783772;