Genetic Variant ENSG00000310037:n.329-4206T>C (chr22-46145351-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000846710.1(ENSG00000310037):n.329-4206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,772 control chromosomes in the GnomAD database, including 21,415 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 0.50 ( 21415 hom., cov: 30)

Consequence

ENSG00000310037
ENST00000846710.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.329

Publications

15 publications found

Variant links:

Genes affected

ENSG00000310037 (HGNC:):

ENSG00000310037 links:

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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 (AFR) allele frequency at 95% confidence interval = 0.749 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
ENSG00000310037	ENST00000846710.1 link	n.329-4206T>C		intron_variant	Intron 1 of 2
ENSG00000310037	ENST00000846711.1 link	n.311+400T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76413

AN:

151654

Hom.:

21367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.755

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.445

Gnomad OTH

AF:

0.459

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

GnomAD4 genome

AF:

0.504

AC:

76514

AN:

151772

Hom.:

21415

Cov.:

AF XY:

0.494

AC XY:

36624

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.756

AC:

31264

AN:

41368

American (AMR)

AF:

0.361

AC:

5508

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.306

AC:

1061

AN:

3468

East Asian (EAS)

AF:

0.200

AC:

1024

AN:

5122

South Asian (SAS)

AF:

0.354

AC:

1707

AN:

4816

European-Finnish (FIN)

AF:

0.399

AC:

4184

AN:

10480

Middle Eastern (MID)

AF:

0.322

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.445

AC:

30241

AN:

67958

Other (OTH)

AF:

0.453

AC:

954

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1684

3369

5053

6738

8422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.453

Hom.:

27613

Bravo

AF:

0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.50

(source)

PhyloP100

-0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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22-46145351-A-G

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