dbSNP rs11752069: ENSG00000230960:n.154+275C>G (chr6-170262141-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 ENST00000452071.1(ENSG00000230960):n.154+275C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,114 control chromosomes in the GnomAD database, including 5,789 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 ( 5789 hom., cov: 32)

Consequence

ENSG00000230960
ENST00000452071.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.419

Publications

2 publications found

Variant links:

Genes affected

ENSG00000230960 (HGNC:):

ENSG00000230960 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC154449	NR_002787.2 link	n.154+275C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230960	ENST00000452071.1 link	n.154+275C>G	intron_variant	Intron 1 of 2	2
ENSG00000230960	ENST00000691159.1 link	n.318+275C>G	intron_variant	Intron 1 of 2
ENSG00000230960	ENST00000701245.2 link	n.318+275C>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40320

AN:

151996

Hom.:

5783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.248

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

GnomAD4 genome

AF:

0.265

AC:

40342

AN:

152114

Hom.:

5789

Cov.:

AF XY:

0.269

AC XY:

20028

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.163

AC:

6762

AN:

41508

American (AMR)

AF:

0.337

AC:

5158

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1037

AN:

3466

East Asian (EAS)

AF:

0.110

AC:

571

AN:

5170

South Asian (SAS)

AF:

0.334

AC:

1612

AN:

4820

European-Finnish (FIN)

AF:

0.321

AC:

3391

AN:

10576

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.309

AC:

21022

AN:

67966

Other (OTH)

AF:

0.246

AC:

518

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1475

2949

4424

5898

7373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.293

Hom.:

841

Bravo

AF:

0.257

Asia WGS

AF:

0.206

AC:

714

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.90

(source)

DANN

Benign

0.49

PhyloP100

-0.42

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