rs774676466

chr17-30237266-AGGGCTGCAGGGGGGATGCTGGGGGTGCAGGGGAGATGCTGGGG-Achr17-30237266-AGGGCTGCAGGGGGGATGCTGGGGGTGCAGGGGAGATGCTGGGG-AGGGCTGCAGGGGGGATGCTGGGGGTGCAGGGGAGATGCTGGGGGGGCTGCAGGGGGGATGCTGGGGGTGCAGGGGAGATGCTGGGG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The XR_001752824.2(LOC105371720):n.280+229_280+271del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency:
  • Genomes: 𝑓 0.28 (2026 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LOC105371720 XR_001752824.2 intron, non_coding_transcript
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.68

Genes affected

LOC105371720 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371720	XR_001752824.2	n.280+229_280+271del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 11592 AN: 40946 Hom.: 2032 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.302

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.283 AC: 11581 AN: 40958 Hom.: 2026 Cov.: 0 AF XY: 0.284 AC XY: 5220 AN XY: 18372

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.299

Alfa AF: 0.192 Hom.: 427

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Serotonin transporter activity, increased/decreased Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 17, 2009

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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: rs774676466; hg19: chr17-28564284;