dbSNP rs1320539: LOC107985255:n.496-112978C>T (chr1-208935148-G-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_001738441.2(LOC107985255):n.496-112978C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 152,174 control chromosomes in the GnomAD database, including 795 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 0.098 ( 795 hom., cov: 33)

Consequence

LOC107985255
XR_001738441.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.339

Publications

2 publications found

Variant links:

Genes affected

LOC107985255 (HGNC:):

LOC107985255 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985255	XR_001738441.2 link	n.496-112978C>T		intron_variant	Intron 1 of 2
LOC107985255	XR_001738442.2 link	n.496-112978C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0980

AC:

14908

AN:

152056

Hom.:

798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0787

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0927

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0991

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.0979

AC:

14905

AN:

152174

Hom.:

795

Cov.:

AF XY:

0.0992

AC XY:

7380

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0785

AC:

3261

AN:

41522

American (AMR)

AF:

0.0925

AC:

1413

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

542

AN:

3470

East Asian (EAS)

AF:

0.151

AC:

782

AN:

5162

South Asian (SAS)

AF:

0.120

AC:

581

AN:

4822

European-Finnish (FIN)

AF:

0.0991

AC:

1050

AN:

10598

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6874

AN:

68000

Other (OTH)

AF:

0.109

AC:

231

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

698

1396

2095

2793

3491

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.102

Hom.:

1495

Bravo

AF:

0.0965

Asia WGS

AF:

0.125

AC:

438

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

0.60

(source)

DANN

Benign

0.41

PhyloP100

-0.34

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