9-16970811-G-T

Variant summary

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

The ENST00000649137.1(ENSG00000237153):n.413-10673G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,952 control chromosomes in the GnomAD database, including 17,576 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 0.47 (17576 hom., cov: 32)
• Consequence: ENST00000649137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649137.1	n.413-10673G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70929 AN: 151834 Hom.: 17555 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.467 AC: 70975 AN: 151952 Hom.: 17576 Cov.: 32 AF XY: 0.467 AC XY: 34710 AN XY: 74252

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.499

Alfa AF: 0.285 Hom.: 642

Bravo AF: 0.482

Asia WGS AF: 0.691 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961511; hg19: chr9-16970809;