dbSNP rs6865651: LOC124901047:n.2086-82177C>T (chr5-113915999-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_007058906.1(LOC124901047):n.2086-82177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,096 control chromosomes in the GnomAD database, including 2,804 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 0.18 ( 2804 hom., cov: 32)

Consequence

LOC124901047
XR_007058906.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115

Publications

1 publications found

Variant links:

COSMIC-nc: COSV60183802

Genes affected

LOC124901047 (HGNC:):

LOC124901047 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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901047	XR_007058906.1 link	n.2086-82177C>T		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27680

AN:

151978

Hom.:

2805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.165

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

GnomAD4 genome

AF:

0.182

AC:

27683

AN:

152096

Hom.:

2804

Cov.:

AF XY:

0.186

AC XY:

13847

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.102

AC:

4245

AN:

41504

American (AMR)

AF:

0.171

AC:

2618

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

598

AN:

3470

East Asian (EAS)

AF:

0.141

AC:

729

AN:

5178

South Asian (SAS)

AF:

0.227

AC:

1098

AN:

4830

European-Finnish (FIN)

AF:

0.296

AC:

3131

AN:

10562

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.215

AC:

14587

AN:

67960

Other (OTH)

AF:

0.164

AC:

347

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1119

2238

3357

4476

5595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.193

Hom.:

475

Bravo

AF:

0.169

Asia WGS

AF:

0.185

AC:

640

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.6

(source)

DANN

Benign

0.51

PhyloP100

-0.12

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