Genetic Variant LOC101927213:n.289-21633G>C (chr2-56627439-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001739478.1(LOC101927213):n.289-21633G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,828 control chromosomes in the GnomAD database, including 15,458 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 0.43 ( 15458 hom., cov: 31)

Consequence

LOC101927213
XR_001739478.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

3 publications found

Variant links:

Genes affected

LOC101927213 (HGNC:):

LOC101927213 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101927213	XR_001739478.1 link	n.289-21633G>C	intron_variant	Intron 4 of 4
LOC101927213	XR_001739479.1 link	n.289-16373G>C	intron_variant	Intron 4 of 4
LOC101927213	XR_001739480.1 link	n.330-16373G>C	intron_variant	Intron 5 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65143

AN:

151710

Hom.:

15454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.244

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.588

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.610

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.514

Gnomad OTH

AF:

0.452

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

GnomAD4 genome

AF:

0.429

AC:

65141

AN:

151828

Hom.:

15458

Cov.:

AF XY:

0.436

AC XY:

32326

AN XY:

74164

show subpopulations

African (AFR)

AF:

0.222

AC:

9199

AN:

41414

American (AMR)

AF:

0.417

AC:

6345

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1591

AN:

3466

East Asian (EAS)

AF:

0.588

AC:

3026

AN:

5148

South Asian (SAS)

AF:

0.495

AC:

2387

AN:

4818

European-Finnish (FIN)

AF:

0.610

AC:

6419

AN:

10526

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.514

AC:

34891

AN:

67912

Other (OTH)

AF:

0.454

AC:

957

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1758

3516

5273

7031

8789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

626

1252

1878

2504

3130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.341

Hom.:

999

Bravo

AF:

0.405

Asia WGS

AF:

0.490

AC:

1702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.17

(source)

DANN

Benign

0.54

PhyloP100

-1.5

Splicing

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

Publications

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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