Genetic Variant LOC105371742:n.354-31410T>G (chr17-34793767-A-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_001752843.3(LOC105371742):n.354-31410T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,192 control chromosomes in the GnomAD database, including 790 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 0.087 ( 790 hom., cov: 32)

Consequence

LOC105371742
XR_001752843.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

3 publications found

Variant links:

Genes affected

LOC105371742 (HGNC:):

LOC105371742 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105371742	XR_001752843.3 link	n.354-31410T>G	intron_variant	Intron 3 of 3
LOC105371742	XR_001752844.3 link	n.354-31410T>G	intron_variant	Intron 3 of 4
LOC105371742	XR_001752845.3 link	n.354-31410T>G	intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0870

AC:

13229

AN:

152074

Hom.:

789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0213

Gnomad AMI

AF:

0.0703

Gnomad AMR

AF:

0.0888

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.0137

Gnomad SAS

AF:

0.0670

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0919

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

GnomAD4 genome

AF:

0.0869

AC:

13225

AN:

152192

Hom.:

790

Cov.:

AF XY:

0.0894

AC XY:

6651

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0213

AC:

883

AN:

41550

American (AMR)

AF:

0.0890

AC:

1360

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

486

AN:

3472

East Asian (EAS)

AF:

0.0135

AC:

AN:

5184

South Asian (SAS)

AF:

0.0670

AC:

323

AN:

4818

European-Finnish (FIN)

AF:

0.177

AC:

1873

AN:

10602

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7953

AN:

67970

Other (OTH)

AF:

0.0909

AC:

192

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

595

1190

1786

2381

2976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.105

Hom.:

1132

Bravo

AF:

0.0762

Asia WGS

AF:

0.0470

AC:

165

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.8

(source)

DANN

Benign

0.72

PhyloP100

1.3

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