dbSNP rs10516800: ENSG00000307815:n.85+3201C>G (chr4-87970438-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000829025.1(ENSG00000307815):n.85+3201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,082 control chromosomes in the GnomAD database, including 5,609 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 0.27 ( 5609 hom., cov: 32)

Consequence

ENSG00000307815
ENST00000829025.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787

Publications

7 publications found

Variant links:

Genes affected

ENSG00000307815 (HGNC:):

ENSG00000307815 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900730	XR_007058172.1 link	n.131+3201C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307815	ENST00000829025.1 link	n.85+3201C>G	intron_variant	Intron 1 of 3
ENSG00000307815	ENST00000829040.1 link	n.105+3201C>G	intron_variant	Intron 1 of 1
ENSG00000307815	ENST00000829041.1 link	n.96+3201C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40941

AN:

151964

Hom.:

5606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.355

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.278

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

GnomAD4 genome

AF:

0.269

AC:

40979

AN:

152082

Hom.:

5609

Cov.:

AF XY:

0.275

AC XY:

20467

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.265

AC:

11000

AN:

41494

American (AMR)

AF:

0.282

AC:

4313

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

844

AN:

3460

East Asian (EAS)

AF:

0.370

AC:

1914

AN:

5166

South Asian (SAS)

AF:

0.206

AC:

995

AN:

4820

European-Finnish (FIN)

AF:

0.355

AC:

3749

AN:

10568

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17142

AN:

67980

Other (OTH)

AF:

0.278

AC:

587

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1560

3121

4681

6242

7802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.264

Hom.:

699

Bravo

AF:

0.262

Asia WGS

AF:

0.275

AC:

954

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.25

(source)

DANN

Benign

0.44

PhyloP100

-0.79

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