9-105026971-A-G

Variant summary

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

The ENST00000666856.1(ENSG00000286536):n.1858-84T>C 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 0.598 in 151,756 control chromosomes in the GnomAD database, including 27,446 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 0.60 (27446 hom., cov: 30)
• Consequence: ENST00000666856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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
	ENST00000666856.1	n.1858-84T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90753 AN: 151638 Hom.: 27438 Cov.: 30

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.598 AC: 90801 AN: 151756 Hom.: 27446 Cov.: 30 AF XY: 0.596 AC XY: 44181 AN XY: 74144

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.604

Alfa AF: 0.639 Hom.: 54131

Bravo AF: 0.596

Asia WGS AF: 0.573 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs328879; hg19: chr9-107789252;