Genetic Variant ENST00000779754.1:n.359-606C>T (chr1-110753052-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 ENST00000779754.1(ENSG00000301570):n.359-606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,140 control chromosomes in the GnomAD database, including 3,794 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 0.20 ( 3794 hom., cov: 32)

Consequence

ENSG00000301570
ENST00000779754.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301570 (HGNC:):

ENSG00000301570 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904296	XR_007066362.1 link	n.22-606C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301570	ENST00000779754.1 link	n.359-606C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30612

AN:

152022

Hom.:

3797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0633

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.201

AC:

30600

AN:

152140

Hom.:

3794

Cov.:

AF XY:

0.204

AC XY:

15132

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0631

AC:

2620

AN:

41516

American (AMR)

AF:

0.240

AC:

3672

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.401

AC:

1394

AN:

3472

East Asian (EAS)

AF:

0.136

AC:

706

AN:

5180

South Asian (SAS)

AF:

0.197

AC:

951

AN:

4828

European-Finnish (FIN)

AF:

0.275

AC:

2905

AN:

10562

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17429

AN:

67988

Other (OTH)

AF:

0.243

AC:

512

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1204

2409

3613

4818

6022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<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:

0.236

Hom.:

9063

Bravo

AF:

0.196

Asia WGS

AF:

0.234

AC:

817

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.2

(source)

DANN

Benign

0.64

PhyloP100

-0.097

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