rs1464666

chr9-104530716-C-Achr9-104530716-C-Gchr9-104530716-C-T

Variant summary

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

The ENST00000668299.1(ENSG00000283001):n.112-5210C>A 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 0.397 in 151,866 control chromosomes in the GnomAD database, including 12,483 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 0.40 (12483 hom., cov: 32)
• Consequence: ENST00000668299.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987105	XR_007061705.1	n.635-384G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668299.1	n.112-5210C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60201 AN: 151750 Hom.: 12470 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.397 AC: 60261 AN: 151866 Hom.: 12483 Cov.: 32 AF XY: 0.404 AC XY: 29979 AN XY: 74226

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.390

Alfa AF: 0.359 Hom.: 4966

Bravo AF: 0.394

Asia WGS AF: 0.621 AC: 2155 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.5
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464666; hg19: chr9-107292997;