dbSNP rs10953515: ENSG00000243797:n.109-42773C>T (chr7-106653236-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 ENST00000490856.5(ENSG00000243797):n.109-42773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,088 control chromosomes in the GnomAD database, including 5,447 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 0.25 ( 5447 hom., cov: 32)

Consequence

ENSG00000243797
ENST00000490856.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

5 publications found

Variant links:

Genes affected

ENSG00000243797 (HGNC:):

ENSG00000243797 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243797	ENST00000490856.5 link	n.109-42773C>T		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1 link	n.173-42773C>T		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38148

AN:

151970

Hom.:

5443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.265

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

GnomAD4 genome

AF:

0.251

AC:

38172

AN:

152088

Hom.:

5447

Cov.:

AF XY:

0.254

AC XY:

18855

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.109

AC:

4521

AN:

41494

American (AMR)

AF:

0.370

AC:

5652

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

1034

AN:

3468

East Asian (EAS)

AF:

0.244

AC:

1259

AN:

5168

South Asian (SAS)

AF:

0.261

AC:

1263

AN:

4830

European-Finnish (FIN)

AF:

0.285

AC:

3021

AN:

10588

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20517

AN:

67960

Other (OTH)

AF:

0.265

AC:

559

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1431

2862

4294

5725

7156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.283

Hom.:

4403

Bravo

AF:

0.252

Asia WGS

AF:

0.241

AC:

835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

(source)

DANN

Benign

0.32

PhyloP100

-0.011

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