Genetic Variant XR_001739693.1:n.211-34679T>G (chr2-126571196-A-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_001739693.1(LOC105373602):n.211-34679T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,192 control chromosomes in the GnomAD database, including 7,113 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 0.26 ( 7113 hom., cov: 33)

Consequence

LOC105373602
XR_001739693.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

2 publications found

Variant links:

Genes affected

LOC105373602 (HGNC:):

LOC105373602 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373602	XR_001739693.1 link	n.211-34679T>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39901

AN:

152074

Hom.:

7082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.0275

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.221

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

GnomAD4 genome

AF:

0.263

AC:

39986

AN:

152192

Hom.:

7113

Cov.:

AF XY:

0.258

AC XY:

19180

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.509

AC:

21113

AN:

41486

American (AMR)

AF:

0.154

AC:

2360

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

484

AN:

3472

East Asian (EAS)

AF:

0.0276

AC:

143

AN:

5184

South Asian (SAS)

AF:

0.105

AC:

505

AN:

4830

European-Finnish (FIN)

AF:

0.175

AC:

1852

AN:

10598

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.189

AC:

12885

AN:

68004

Other (OTH)

AF:

0.218

AC:

461

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1346

2692

4038

5384

6730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<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:

0.174

Hom.:

1279

Bravo

AF:

0.273

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.0

(source)

DANN

Benign

0.41

PhyloP100

-1.1

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