rs3834363

chr8-81484005-GGT-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000524085.2(ENSG00000253859):n.299-13906_299-13905del 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 0.355 in 149,158 control chromosomes in the GnomAD database, including 10,422 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10422 hom., cov: 0)
• Consequence: ENST00000524085.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927118	XR_001745980.2	n.517+22037_517+22038del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000524085.2	n.299-13906_299-13905del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.355 AC: 52872 AN: 149048 Hom.: 10394 Cov.: 0

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.355 AC: 52954 AN: 149158 Hom.: 10422 Cov.: 0 AF XY: 0.352 AC XY: 25725 AN XY: 73028

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.344

Alfa AF: 0.329 Hom.: 1130

Bravo AF: 0.392

Asia WGS AF: 0.506 AC: 1756 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3834363; hg19: chr8-82396240;