9-108407724-TAAAC-TAAACAAAC

Position:

• chr9-108407724-TAAAC-TAAACAAAC

Variant summary

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

The XR_007061722.1(LOC105376214):​n.326-32129_326-32128insGTTT variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13369 hom., cov: 0)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.326-32129_326-32128insGTTT		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.326-32129_326-32128insGTTT		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.326-32129_326-32128insGTTT		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.410 AC: 61420 AN: 149828 Hom.: 13367 Cov.: 0

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.410 AC: 61440 AN: 149942 Hom.: 13369 Cov.: 0 AF XY: 0.405 AC XY: 29687 AN XY: 73268

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.456

Alfa AF: 0.419 Hom.: 1502

Bravo AF: 0.392

Asia WGS AF: 0.232 AC: 809 AN: 3478

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: rs2307745; hg19: chr9-111170004;