dbSNP rs6707038: ENSG00000288857:n.260-900C>T (chr2-237924622-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 ENST00000686788.2(ENSG00000288857):n.260-900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,066 control chromosomes in the GnomAD database, including 28,547 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 0.61 ( 28547 hom., cov: 33)

Consequence

ENSG00000288857
ENST00000686788.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.660

Publications

4 publications found

Variant links:

Genes affected

ENSG00000288857 (HGNC:):

ENSG00000288857 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373960	XR_924046.3 link	n.75-900C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288857	ENST00000686788.2 link	n.260-900C>T	intron_variant	Intron 1 of 1
ENSG00000288857	ENST00000848167.1 link	n.221-900C>T	intron_variant	Intron 2 of 5
ENSG00000288857	ENST00000848168.1 link	n.135-900C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92331

AN:

151948

Hom.:

28504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.640

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.650

Gnomad SAS

AF:

0.579

Gnomad FIN

AF:

0.762

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.608

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

GnomAD4 genome

AF:

0.608

AC:

92433

AN:

152066

Hom.:

28547

Cov.:

AF XY:

0.620

AC XY:

46063

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.640

AC:

26524

AN:

41452

American (AMR)

AF:

0.640

AC:

9778

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.653

AC:

2268

AN:

3472

East Asian (EAS)

AF:

0.650

AC:

3363

AN:

5174

South Asian (SAS)

AF:

0.579

AC:

2792

AN:

4818

European-Finnish (FIN)

AF:

0.762

AC:

8067

AN:

10584

Middle Eastern (MID)

AF:

0.619

AC:

182

AN:

294

European-Non Finnish (NFE)

AF:

0.554

AC:

37655

AN:

67980

Other (OTH)

AF:

0.611

AC:

1292

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1863

3727

5590

7454

9317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.565

Hom.:

43423

Bravo

AF:

0.598

Asia WGS

AF:

0.628

AC:

2185

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.73

(source)

DANN

Benign

0.77

PhyloP100

-0.66

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