Genetic Variant XR_001737665.2:n.28-2807G>A (chr1-70827508-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001737665.2(LOC102724572):n.28-2807G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,898 control chromosomes in the GnomAD database, including 9,134 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 0.34 ( 9134 hom., cov: 32)

Consequence

LOC102724572
XR_001737665.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Publications

4 publications found

Variant links:

Genes affected

LOC102724572 (HGNC:):

LOC102724572 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724572	XR_001737665.2 link	n.28-2807G>A		intron_variant	Intron 1 of 4
LOC102724572	XR_426711.4 link	n.238-11291G>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51456

AN:

151782

Hom.:

9127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.395

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.357

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

GnomAD4 genome

AF:

0.339

AC:

51485

AN:

151898

Hom.:

9134

Cov.:

AF XY:

0.336

AC XY:

24917

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.266

AC:

11007

AN:

41424

American (AMR)

AF:

0.319

AC:

4868

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.454

AC:

1573

AN:

3468

East Asian (EAS)

AF:

0.175

AC:

902

AN:

5158

South Asian (SAS)

AF:

0.263

AC:

1266

AN:

4814

European-Finnish (FIN)

AF:

0.398

AC:

4189

AN:

10514

Middle Eastern (MID)

AF:

0.403

AC:

117

AN:

290

European-Non Finnish (NFE)

AF:

0.390

AC:

26497

AN:

67954

Other (OTH)

AF:

0.353

AC:

743

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1702

3404

5107

6809

8511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.356

Hom.:

1613

Bravo

AF:

0.332

Asia WGS

AF:

0.192

AC:

670

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

(source)

DANN

Benign

0.28

PhyloP100

1.0

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