Genetic Variant LOC124901704:n.132-7603C>G (chr7-97187952-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_007060445.1(LOC124901704):n.132-7603C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,102 control chromosomes in the GnomAD database, including 5,727 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 0.25 ( 5727 hom., cov: 32)

Consequence

LOC124901704
XR_007060445.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.141

Publications

1 publications found

Variant links:

Genes affected

LOC124901704 (HGNC:):

LOC124901704 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901704	XR_007060445.1 link	n.132-7603C>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38317

AN:

151986

Hom.:

5731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0949

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.269

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

GnomAD4 genome

AF:

0.252

AC:

38294

AN:

152102

Hom.:

5727

Cov.:

AF XY:

0.252

AC XY:

18703

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0947

AC:

3932

AN:

41522

American (AMR)

AF:

0.206

AC:

3152

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

1323

AN:

3470

East Asian (EAS)

AF:

0.383

AC:

1980

AN:

5172

South Asian (SAS)

AF:

0.294

AC:

1416

AN:

4816

European-Finnish (FIN)

AF:

0.308

AC:

3252

AN:

10546

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.327

AC:

22227

AN:

67972

Other (OTH)

AF:

0.266

AC:

563

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1411

2822

4232

5643

7054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.190

Hom.:

455

Bravo

AF:

0.239

Asia WGS

AF:

0.300

AC:

1042

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.83

(source)

DANN

Benign

0.62

PhyloP100

-0.14

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