Genetic Variant LOC105376412:n.281+769T>G (chr10-11677011-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_930661.3(LOC105376412):n.135-2248T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,176 control chromosomes in the GnomAD database, including 3,819 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 0.22 ( 3819 hom., cov: 32)

Consequence

LOC105376412
XR_930661.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Variant links:

Genes affected

LOC105376412 (HGNC:):

LOC105376412 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376412	XR_002957063.2 link	n.281+769T>G	intron_variant	Intron 2 of 3
LOC105376413	XR_007062054.1 link	n.1203+2863A>C	intron_variant	Intron 3 of 6
LOC105376412	XR_007062055.1 link	n.760+290T>G	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32820

AN:

152058

Hom.:

3819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.0860

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.212

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

GnomAD4 genome

AF:

0.216

AC:

32822

AN:

152176

Hom.:

3819

Cov.:

AF XY:

0.211

AC XY:

15675

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.160

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.0858

Gnomad4 SAS

AF:

0.238

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.242

Hom.:

4434

Bravo

AF:

0.209

Asia WGS

AF:

0.135

AC:

472

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.3

DANN

Benign

0.68

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