dbSNP rs10498902: ENSG00000272243:n.89+37474C>T (chr6-74768915-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 ENST00000740411.1(ENSG00000272243):n.89+37474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 152,274 control chromosomes in the GnomAD database, including 102 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 0.014 ( 102 hom., cov: 32)

Consequence

ENSG00000272243
ENST00000740411.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452

Publications

0 publications found

Variant links:

Genes affected

ENSG00000272243 (HGNC:):

ENSG00000272243 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 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
ENSG00000272243	ENST00000740411.1 link	n.89+37474C>T		intron_variant	Intron 1 of 2
ENSG00000272243	ENST00000740412.1 link	n.44+37474C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0139

AC:

2112

AN:

152156

Hom.:

102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.0741

Gnomad FIN

AF:

0.00499

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00482

Gnomad OTH

AF:

0.0191

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

GnomAD4 genome

AF:

0.0138

AC:

2108

AN:

152274

Hom.:

102

Cov.:

AF XY:

0.0166

AC XY:

1237

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.00125

AC:

AN:

41576

American (AMR)

AF:

0.0364

AC:

557

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.136

AC:

703

AN:

5176

South Asian (SAS)

AF:

0.0740

AC:

356

AN:

4812

European-Finnish (FIN)

AF:

0.00499

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00482

AC:

328

AN:

68004

Other (OTH)

AF:

0.0194

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

191

287

382

478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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:

0.00731

Hom.:

Bravo

AF:

0.0145

Asia WGS

AF:

0.0990

AC:

343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.7

(source)

DANN

Benign

0.19

PhyloP100

0.45

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