Genetic Variant LOC105377724:n.1633+1677A>G (chr5-171724227-T-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_001742983.2(LOC105377724):n.1633+1677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,068 control chromosomes in the GnomAD database, including 9,504 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 0.35 ( 9504 hom., cov: 32)

Consequence

LOC105377724
XR_001742983.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

7 publications found

Variant links:

Genes affected

LOC105377724 (HGNC:):

LOC105377724 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377724	XR_001742983.2 link	n.1633+1677A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285914	ENST00000803459.1 link	n.*47A>G	downstream_gene_variant
ENSG00000285914	ENST00000803460.1 link	n.*41A>G	downstream_gene_variant
ENSG00000285914	ENST00000803461.1 link	n.*113A>G	downstream_gene_variant
ENSG00000285914	ENST00000803462.1 link	n.*113A>G	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53419

AN:

151952

Hom.:

9496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.365

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.347

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

GnomAD4 genome

AF:

0.351

AC:

53444

AN:

152068

Hom.:

9504

Cov.:

AF XY:

0.352

AC XY:

26166

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.398

AC:

16514

AN:

41472

American (AMR)

AF:

0.374

AC:

5706

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

932

AN:

3472

East Asian (EAS)

AF:

0.364

AC:

1881

AN:

5174

South Asian (SAS)

AF:

0.215

AC:

1036

AN:

4818

European-Finnish (FIN)

AF:

0.364

AC:

3841

AN:

10560

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.330

AC:

22428

AN:

67990

Other (OTH)

AF:

0.345

AC:

730

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1752

3504

5257

7009

8761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.336

Hom.:

26282

Bravo

AF:

0.358

Asia WGS

AF:

0.259

AC:

903

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.9

(source)

DANN

Benign

0.74

PhyloP100

-1.5

Splicing

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

Publications

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5-171724227-T-C

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