Genetic Variant ENST00000762835.1:n.72_80delAAGAAAACG (chr1-223108950-TGAAGAAAAC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000762835.1(ENSG00000299361):n.72_80delAAGAAAACG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9813 hom., cov: 0)

Consequence

ENSG00000299361
ENST00000762835.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

Publications

0 publications found

Variant links:

Genes affected

ENSG00000299361 (HGNC:):

ENSG00000299361 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299361	ENST00000762835.1 link	n.72_80delAAGAAAACG	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000299361	ENST00000762836.1 link	n.173_181delAAGAAAACG	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000299361	ENST00000762837.1 link	n.173_181delAAGAAAACG	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50845

AN:

151558

Hom.:

9810

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.333

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

GnomAD4 genome

AF:

0.335

AC:

50874

AN:

151674

Hom.:

9813

Cov.:

AF XY:

0.338

AC XY:

25059

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.144

AC:

5971

AN:

41450

American (AMR)

AF:

0.323

AC:

4921

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.401

AC:

1391

AN:

3468

East Asian (EAS)

AF:

0.208

AC:

1069

AN:

5144

South Asian (SAS)

AF:

0.422

AC:

2018

AN:

4782

European-Finnish (FIN)

AF:

0.493

AC:

5186

AN:

10526

Middle Eastern (MID)

AF:

0.380

AC:

111

AN:

292

European-Non Finnish (NFE)

AF:

0.429

AC:

29061

AN:

67764

Other (OTH)

AF:

0.333

AC:

700

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

1481

2962

4443

5924

7405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.389

Hom.:

1497

Bravo

AF:

0.311

Asia WGS

AF:

0.301

AC:

1046

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.4

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