dbSNP rs72647484: ENSG00000294752:n.412-11571T>C (chr1-22261235-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000725701.1(ENSG00000294752):n.412-11571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,196 control chromosomes in the GnomAD database, including 403 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 0.062 ( 403 hom., cov: 32)

Consequence

ENSG00000294752
ENST00000725701.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

22 publications found

Variant links:

Genes affected

ENSG00000294752 (HGNC:):

ENSG00000294752 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000294752	ENST00000725701.1 link	n.412-11571T>C	intron_variant	Intron 3 of 3
ENSG00000294752	ENST00000725702.1 link	n.236-11571T>C	intron_variant	Intron 2 of 2
ENSG00000294752	ENST00000725703.1 link	n.394-11571T>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0616

AC:

9374

AN:

152078

Hom.:

405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0152

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.0484

Gnomad ASJ

AF:

0.0666

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0211

Gnomad FIN

AF:

0.0892

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0947

Gnomad OTH

AF:

0.0618

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

GnomAD4 genome

AF:

0.0616

AC:

9372

AN:

152196

Hom.:

403

Cov.:

AF XY:

0.0593

AC XY:

4409

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.0152

AC:

630

AN:

41540

American (AMR)

AF:

0.0483

AC:

738

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0666

AC:

231

AN:

3470

East Asian (EAS)

AF:

0.000580

AC:

AN:

5172

South Asian (SAS)

AF:

0.0210

AC:

101

AN:

4820

European-Finnish (FIN)

AF:

0.0892

AC:

946

AN:

10604

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0947

AC:

6441

AN:

67984

Other (OTH)

AF:

0.0616

AC:

130

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

449

898

1346

1795

2244

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0823

Hom.:

817

Bravo

AF:

0.0571

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.49

(source)

DANN

Benign

0.62

PhyloP100

-1.2

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