Variant 2-127133887-T-TGGG details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_923311.4(LOC105373605):n.910+588_910+590dup 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 0.30 ( 7024 hom., cov: 0)

Consequence

LOC105373605
XR_923311.4 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396

Variant links:

Genes affected

LOC105373605 (HGNC:):

LOC105373605 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4 linkuse as main transcript	n.910+588_910+590dup		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3 linkuse as main transcript	n.513+588_513+590dup		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45400

AN:

150912

Hom.:

6994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.287

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

GnomAD4 genome

AF:

0.301

AC:

45478

AN:

151028

Hom.:

7024

Cov.:

AF XY:

0.298

AC XY:

21973

AN XY:

73774

show subpopulations

Gnomad4 AFR

AF:

0.349

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.334

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.121

Hom.:

194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over