dbSNP rs13375144: LOC100996886:n.196872560C>T (chr1-196872560-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 variant allele was found at a frequency of 0.211 in 151,154 control chromosomes in the GnomAD database, including 5,294 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 0.21 ( 5294 hom., cov: 32)

Consequence

LOC100996886
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

5 publications found

Variant links:

Genes affected

LOC100996886 (HGNC:):

LOC100996886 links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196872560C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1 link	n.427-12046C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

31840

AN:

151040

Hom.:

5288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.000967

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0939

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.213

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

GnomAD4 genome

AF:

0.211

AC:

31870

AN:

151154

Hom.:

5294

Cov.:

AF XY:

0.208

AC XY:

15394

AN XY:

73892

show subpopulations

African (AFR)

AF:

0.435

AC:

17774

AN:

40834

American (AMR)

AF:

0.140

AC:

2132

AN:

15180

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

404

AN:

3468

East Asian (EAS)

AF:

0.000969

AC:

AN:

5158

South Asian (SAS)

AF:

0.161

AC:

774

AN:

4808

European-Finnish (FIN)

AF:

0.0939

AC:

987

AN:

10506

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9195

AN:

67896

Other (OTH)

AF:

0.210

AC:

442

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1106

2213

3319

4426

5532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.181

Hom.:

749

Bravo

AF:

0.223

Asia WGS

AF:

0.0900

AC:

315

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

(source)

DANN

Benign

0.22

PhyloP100

-1.5

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

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rs13375144

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