dbSNP rs6683868: ENSG00000307102:n.112+5720C>T (chr1-19049347-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 ENST00000823875.1(ENSG00000307102):n.112+5720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,276 control chromosomes in the GnomAD database, including 1,036 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 0.11 ( 1036 hom., cov: 33)

Consequence

ENSG00000307102
ENST00000823875.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

6 publications found

Variant links:

Genes affected

ENSG00000307102 (HGNC:):

ENSG00000307102 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=-0.91).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376815	XR_947015.2 link	n.551+1531C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307102	ENST00000823875.1 link	n.112+5720C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16034

AN:

152158

Hom.:

1033

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.0619

Gnomad ASJ

AF:

0.0593

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0261

Gnomad FIN

AF:

0.0453

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.104

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

GnomAD4 genome

AF:

0.105

AC:

16059

AN:

152276

Hom.:

1036

Cov.:

AF XY:

0.102

AC XY:

7565

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.170

AC:

7076

AN:

41524

American (AMR)

AF:

0.0618

AC:

945

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0593

AC:

206

AN:

3472

East Asian (EAS)

AF:

0.000578

AC:

AN:

5186

South Asian (SAS)

AF:

0.0259

AC:

125

AN:

4832

European-Finnish (FIN)

AF:

0.0453

AC:

481

AN:

10614

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6904

AN:

68028

Other (OTH)

AF:

0.103

AC:

218

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

715

1429

2144

2858

3573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.101

Hom.:

2931

Bravo

AF:

0.111

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.71

(source)

DANN

Benign

0.59

PhyloP100

-0.011

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