Genetic Variant LOC105371675:n.257+4762G>A (chr1-196928695-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007066779.1(LOC105371675):n.257+4762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 ( 554 hom., cov: 9)

Consequence

LOC105371675
XR_007066779.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

1 publications found

Variant links:

Genes affected

LOC105371675 (HGNC:):

LOC105371675 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371675	XR_007066779.1 link	n.257+4762G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

10031

AN:

69010

Hom.:

555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.0517

Gnomad SAS

AF:

0.0967

Gnomad FIN

AF:

0.0706

Gnomad MID

AF:

0.0603

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.143

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

GnomAD4 genome

AF:

0.145

AC:

10032

AN:

69000

Hom.:

554

Cov.:

AF XY:

0.143

AC XY:

4586

AN XY:

32096

show subpopulations

African (AFR)

AF:

0.221

AC:

2839

AN:

12822

American (AMR)

AF:

0.198

AC:

1251

AN:

6326

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

191

AN:

1772

East Asian (EAS)

AF:

0.0518

AC:

AN:

1640

South Asian (SAS)

AF:

0.0967

AC:

183

AN:

1892

European-Finnish (FIN)

AF:

0.0706

AC:

221

AN:

3132

Middle Eastern (MID)

AF:

0.0588

AC:

AN:

102

European-Non Finnish (NFE)

AF:

0.128

AC:

5085

AN:

39788

Other (OTH)

AF:

0.142

AC:

135

AN:

950

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.412

Heterozygous variant carriers

324

648

972

1296

1620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.52

(source)

DANN

Benign

0.070

PhyloP100

0.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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