dbSNP rs230271: LOC105378667:n.287+493C>A (chr1-39824925-C-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_947221.3(LOC105378667):n.287+493C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,960 control chromosomes in the GnomAD database, including 25,666 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 0.56 ( 25666 hom., cov: 32)

Consequence

LOC105378667
XR_947221.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.579

Publications

7 publications found

Variant links:

Genes affected

LOC105378667 (HGNC:):

LOC105378667 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378667	XR_947221.3 link	n.287+493C>A		intron_variant	Intron 1 of 3
LOC105378667	XR_947222.3 link	n.-242C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000301696	ENST00000780948.1 link	n.-196C>A	upstream_gene_variant
ENSG00000301696	ENST00000780949.1 link	n.-224C>A	upstream_gene_variant
ENSG00000301696	ENST00000780950.1 link	n.-233C>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

84971

AN:

151842

Hom.:

25612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.801

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.480

Gnomad EAS

AF:

0.646

Gnomad SAS

AF:

0.471

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.523

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

GnomAD4 genome

AF:

0.560

AC:

85081

AN:

151960

Hom.:

25666

Cov.:

AF XY:

0.558

AC XY:

41424

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.802

AC:

33230

AN:

41452

American (AMR)

AF:

0.493

AC:

7533

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

1665

AN:

3466

East Asian (EAS)

AF:

0.646

AC:

3337

AN:

5164

South Asian (SAS)

AF:

0.470

AC:

2266

AN:

4820

European-Finnish (FIN)

AF:

0.474

AC:

4990

AN:

10530

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.450

AC:

30549

AN:

67948

Other (OTH)

AF:

0.523

AC:

1102

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1722

3445

5167

6890

8612

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<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:

0.477

Hom.:

30075

Bravo

AF:

0.574

Asia WGS

AF:

0.605

AC:

2105

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.56

(source)

DANN

Benign

0.59

PhyloP100

-0.58

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