dbSNP rs10495214: LOC105373281:n.340+5980A>C (chr1-223684792-T-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_949164.2(LOC105373281):n.340+5980A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,138 control chromosomes in the GnomAD database, including 775 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 0.069 ( 775 hom., cov: 32)

Consequence

LOC105373281
XR_949164.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.985

Publications

2 publications found

Variant links:

Genes affected

LOC105373281 (HGNC:):

LOC105373281 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105373281	XR_949164.2 link	n.340+5980A>C	intron_variant	Intron 2 of 2
LOC105373281	XR_949165.2 link	n.407+5980A>C	intron_variant	Intron 2 of 2
LOC105373281	XR_949166.2 link	n.96+5980A>C	intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0684

AC:

10405

AN:

152020

Hom.:

768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.0782

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.0383

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.00828

Gnomad FIN

AF:

0.0157

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.0731

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

GnomAD4 genome

AF:

0.0686

AC:

10435

AN:

152138

Hom.:

775

Cov.:

AF XY:

0.0706

AC XY:

5252

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.134

AC:

5556

AN:

41484

American (AMR)

AF:

0.173

AC:

2639

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0383

AC:

133

AN:

3472

East Asian (EAS)

AF:

0.167

AC:

862

AN:

5172

South Asian (SAS)

AF:

0.00787

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0157

AC:

167

AN:

10604

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0118

AC:

802

AN:

67998

Other (OTH)

AF:

0.0747

AC:

158

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

431

862

1292

1723

2154

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:

0.0339

Hom.:

1090

Bravo

AF:

0.0888

Asia WGS

AF:

0.0970

AC:

337

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.90

(source)

DANN

Benign

0.44

PhyloP100

-0.98

Splicing

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