chr3-117509776-G-GTGGGAATTTGAATATTATAACAGATCC

Position:

• chr3-117509776-G-GTGGGAATTTGAATATTATAACAGATCC

Variant summary

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

The XR_924361.3(LOC105374056):​n.26459_26485dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 150,732 control chromosomes in the GnomAD database, including 14,183 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (14183 hom., cov: 24)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374056	XR_924361.3	n.26459_26485dup		non_coding_transcript_exon_variant	1/4
LOC105374056	XR_007096021.1	n.26459_26485dup		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.391 AC: 58930 AN: 150616 Hom.: 14188 Cov.: 24

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.391 AC: 58904 AN: 150732 Hom.: 14183 Cov.: 24 AF XY: 0.385 AC XY: 28309 AN XY: 73558

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.403

Alfa AF: 0.374 Hom.: 1322

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: rs45617832; hg19: chr3-117228623;