Genetic Variant XR_002956518.2:n.1531-5706A>G (chr7-140933681-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_002956518.2(LOC105375536):n.1531-5706A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 152,270 control chromosomes in the GnomAD database, including 405 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 0.061 ( 405 hom., cov: 32)

Consequence

LOC105375536
XR_002956518.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

2 publications found

Variant links:

Genes affected

LOC105375536 (HGNC:):

LOC105375536 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375536	XR_002956518.2 link	n.1531-5706A>G		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0607

AC:

9236

AN:

152152

Hom.:

405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0152

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.0558

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0101

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0853

Gnomad OTH

AF:

0.0597

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

GnomAD4 genome

AF:

0.0607

AC:

9238

AN:

152270

Hom.:

405

Cov.:

AF XY:

0.0614

AC XY:

4571

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0152

AC:

632

AN:

41570

American (AMR)

AF:

0.0558

AC:

853

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0905

AC:

314

AN:

3470

East Asian (EAS)

AF:

0.000579

AC:

AN:

5178

South Asian (SAS)

AF:

0.0106

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.123

AC:

1300

AN:

10590

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0853

AC:

5800

AN:

68014

Other (OTH)

AF:

0.0591

AC:

125

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

432

864

1296

1728

2160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0601

Hom.:

136

Bravo

AF:

0.0534

Asia WGS

AF:

0.00953

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.12

(source)

DANN

Benign

0.83

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