Genetic Variant XR_007060535.1:n.29222-39122A>T (chr7-134706212-T-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_007060535.1(LOC124901750):n.29222-39122A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,052 control chromosomes in the GnomAD database, including 6,554 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 0.29 ( 6554 hom., cov: 32)

Consequence

LOC124901750
XR_007060535.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.269

Publications

1 publications found

Variant links:

Genes affected

LOC124901750 (HGNC:):

LOC124901750 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC124901750	XR_007060535.1 link	n.29222-39122A>T	intron_variant	Intron 1 of 2
LOC124901750	XR_007060536.1 link	n.29222-39122A>T	intron_variant	Intron 1 of 2
LOC124901750	XR_007060537.1 link	n.29222-86264A>T	intron_variant	Intron 1 of 1
LOC124901750	XR_007060538.1 link	n.29222-47502A>T	intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44174

AN:

151934

Hom.:

6538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.284

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

GnomAD4 genome

AF:

0.291

AC:

44226

AN:

152052

Hom.:

6554

Cov.:

AF XY:

0.288

AC XY:

21378

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.333

AC:

13793

AN:

41480

American (AMR)

AF:

0.341

AC:

5213

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

864

AN:

3470

East Asian (EAS)

AF:

0.193

AC:

995

AN:

5164

South Asian (SAS)

AF:

0.273

AC:

1315

AN:

4812

European-Finnish (FIN)

AF:

0.200

AC:

2117

AN:

10582

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.279

AC:

18942

AN:

67952

Other (OTH)

AF:

0.281

AC:

592

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1610

3220

4831

6441

8051

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.288

Hom.:

810

Bravo

AF:

0.303

Asia WGS

AF:

0.227

AC:

791

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.4

(source)

DANN

Benign

0.85

PhyloP100

-0.27

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