Genetic Variant XR_007060636.1:n.456-3537C>T (chr7-52421612-C-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_007060636.1(LOC124901810):n.456-3537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,208 control chromosomes in the GnomAD database, including 487 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 0.050 ( 487 hom., cov: 32)

Consequence

LOC124901810
XR_007060636.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.50

Publications

3 publications found

Variant links:

Genes affected

LOC124901810 (HGNC:):

LOC124901810 links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901810	XR_007060636.1 link	n.456-3537C>T		intron_variant	Intron 2 of 3
LOC124901810	XR_007060637.1 link	n.572-3537C>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0496

AC:

7545

AN:

152090

Hom.:

483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0360

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.0491

Gnomad FIN

AF:

0.00283

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00945

Gnomad OTH

AF:

0.0535

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

GnomAD4 genome

AF:

0.0497

AC:

7560

AN:

152208

Hom.:

487

Cov.:

AF XY:

0.0508

AC XY:

3778

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.104

AC:

4333

AN:

41532

American (AMR)

AF:

0.0359

AC:

549

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0101

AC:

AN:

3470

East Asian (EAS)

AF:

0.308

AC:

1585

AN:

5140

South Asian (SAS)

AF:

0.0493

AC:

238

AN:

4826

European-Finnish (FIN)

AF:

0.00283

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00945

AC:

643

AN:

68020

Other (OTH)

AF:

0.0548

AC:

116

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

328

656

984

1312

1640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0261

Hom.:

866

Bravo

AF:

0.0563

Asia WGS

AF:

0.176

AC:

610

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.029

(source)

DANN

Benign

0.52

PhyloP100

-2.5

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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