ENST00000701135.1:n.277+6190T>G

Variant names:

• chr13-21664407-A-C
• rs9634328
• ENST00000701135.1:n.277+6190T>G

Variant summary

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

The ENST00000701135.1(ENSG00000289860):​n.277+6190T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,074 control chromosomes in the GnomAD database, including 7,269 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 0.30 (7269 hom., cov: 32)
• Consequence: ENSG00000289860 ENST00000701135.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

ENSG00000289860 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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
ENSG00000289860	ENST00000701135.1	n.277+6190T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45754 AN: 151956 Hom.: 7264 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.301 AC: 45778 AN: 152074 Hom.: 7269 Cov.: 32 AF XY: 0.301 AC XY: 22404 AN XY: 74354

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.281

Alfa AF: 0.325 Hom.: 4694

Bravo AF: 0.290

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	6.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9634328; hg19: chr13-22238546;