Genetic Variant LOC124902114:n.11101G>A (chr9-5610381-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007061405.1(LOC124902114):n.11101G>A 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 0.311 in 151,966 control chromosomes in the GnomAD database, including 7,914 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 7914 hom., cov: 32)

Consequence

LOC124902114
XR_007061405.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

Variant links:

Genes affected

LOC124902114 (HGNC:):

LOC124902114 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC124902114	XR_007061405.1 link	n.11101G>A	non_coding_transcript_exon_variant	Exon 1 of 3
LOC124902114	XR_007061407.1 link	n.11101G>A	non_coding_transcript_exon_variant	Exon 1 of 4
LOC124902114	XR_007061403.1 link	n.161+19186G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286162	ENST00000650674.2 link	n.226+18409G>A		intron_variant	Intron 1 of 1
ENSG00000286162	ENST00000661858.1 link	n.182+19186G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47252

AN:

151848

Hom.:

7885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.293

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

GnomAD4 genome

AF:

0.311

AC:

47318

AN:

151966

Hom.:

7914

Cov.:

AF XY:

0.316

AC XY:

23495

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.630

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.291

Hom.:

13581

Bravo

AF:

0.327

Asia WGS

AF:

0.474

AC:

1649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

DANN

Benign

0.55

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