ENST00000690140.1:n.308+271T>G

Variant names:

• chr8-8632641-T-G
• rs11782269
• ENST00000690140.1:n.308+271T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690140.1(ENSG00000289622):​n.308+271T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,072 control chromosomes in the GnomAD database, including 5,554 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 0.26 (5554 hom., cov: 32)
• Consequence: ENSG00000289622 ENST00000690140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

ENSG00000289622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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
ENSG00000289622	ENST00000690140.1	n.308+271T>G		intron_variant	Intron 2 of 3
ENSG00000289622	ENST00000701271.1	n.308+271T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40010 AN: 151954 Hom.: 5555 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.263 AC: 40016 AN: 152072 Hom.: 5554 Cov.: 32 AF XY: 0.270 AC XY: 20039 AN XY: 74336

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.244

Alfa AF: 0.256 Hom.: 2341

Bravo AF: 0.244

Asia WGS AF: 0.269 AC: 932 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11782269; hg19: chr8-8490151;