Genetic Variant LOC105378418:n.355+2938G>T (chr10-89197646-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_946180.4(LOC105378418):n.355+2938G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,064 control chromosomes in the GnomAD database, including 7,462 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 0.27 ( 7462 hom., cov: 30)

Consequence

LOC105378418
XR_946180.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322

Publications

6 publications found

Variant links:

Genes affected

LOC105378418 (HGNC:):

LOC105378418 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378418	XR_946180.4 link	n.355+2938G>T		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41292

AN:

150966

Hom.:

7433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.790

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.255

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

GnomAD4 genome

AF:

0.274

AC:

41373

AN:

151064

Hom.:

7462

Cov.:

AF XY:

0.282

AC XY:

20806

AN XY:

73710

show subpopulations

African (AFR)

AF:

0.418

AC:

17188

AN:

41104

American (AMR)

AF:

0.294

AC:

4465

AN:

15208

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

711

AN:

3466

East Asian (EAS)

AF:

0.790

AC:

4056

AN:

5134

South Asian (SAS)

AF:

0.354

AC:

1698

AN:

4792

European-Finnish (FIN)

AF:

0.281

AC:

2868

AN:

10210

Middle Eastern (MID)

AF:

0.247

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.141

AC:

9599

AN:

67854

Other (OTH)

AF:

0.256

AC:

538

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1325

2650

3976

5301

6626

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.186

Hom.:

11479

Bravo

AF:

0.285

Asia WGS

AF:

0.507

AC:

1759

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.41

(source)

DANN

Benign

0.35

PhyloP100

-0.32

Splicing

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

Publications

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10-89197646-G-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over