dbSNP rs1934712: ENSG00000233359:n.136-7643C>T (chr1-102488445-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 ENST00000722514.1(ENSG00000233359):n.136-7643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,798 control chromosomes in the GnomAD database, including 15,996 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 0.43 ( 15996 hom., cov: 31)

Consequence

ENSG00000233359
ENST00000722514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215

Publications

3 publications found

Variant links:

Genes affected

ENSG00000233359 (HGNC:58374):

ENSG00000233359 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000233359	ENST00000722514.1 link	n.136-7643C>T	intron_variant	Intron 2 of 6
ENSG00000233359	ENST00000722515.1 link	n.136-7643C>T	intron_variant	Intron 2 of 3
ENSG00000233359	ENST00000722516.1 link	n.163-7643C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.432

AC:

65500

AN:

151680

Hom.:

15993

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.597

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.462

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

GnomAD4 genome

AF:

0.432

AC:

65519

AN:

151798

Hom.:

15996

Cov.:

AF XY:

0.434

AC XY:

32223

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.182

AC:

7541

AN:

41466

American (AMR)

AF:

0.489

AC:

7438

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.531

AC:

1838

AN:

3462

East Asian (EAS)

AF:

0.426

AC:

2190

AN:

5144

South Asian (SAS)

AF:

0.472

AC:

2270

AN:

4810

European-Finnish (FIN)

AF:

0.575

AC:

6063

AN:

10540

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.538

AC:

36477

AN:

67850

Other (OTH)

AF:

0.465

AC:

983

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1704

3408

5112

6816

8520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.460

Hom.:

3893

Bravo

AF:

0.414

Asia WGS

AF:

0.459

AC:

1593

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.8

(source)

DANN

Benign

0.61

PhyloP100

-0.21

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