ENST00000779509.1:n.139-19870A>G

Variant names:

• chr11-69228491-A-G
• rs7130881
• ENST00000779509.1:n.139-19870A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-19870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,134 control chromosomes in the GnomAD database, including 1,790 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 0.15 (1790 hom., cov: 31)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 50 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 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.139-19870A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22538 AN: 152016 Hom.: 1790 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.148 AC: 22544 AN: 152134 Hom.: 1790 Cov.: 31 AF XY: 0.144 AC XY: 10685 AN XY: 74368

African (AFR) AF: 0.161 AC: 6669 AN: 41500

American (AMR) AF: 0.119 AC: 1817 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3472

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5180

South Asian (SAS) AF: 0.0774 AC: 373 AN: 4822

European-Finnish (FIN) AF: 0.0831 AC: 881 AN: 10600

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.168 AC: 11395 AN: 67978

Other (OTH) AF: 0.175 AC: 368 AN: 2106

Alfa AF: 0.159 Hom.: 9528

Bravo AF: 0.154

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7130881; hg19: chr11-68995958;