Genetic Variant ENST00000634701.1:n.60+3886C>T (chr1-60864031-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 ENST00000634701.1(ENSG00000231252):n.60+3886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0501 in 152,142 control chromosomes in the GnomAD database, including 259 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 0.050 ( 259 hom., cov: 32)

Consequence

ENSG00000231252
ENST00000634701.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

Publications

4 publications found

Variant links:

Genes affected

ENSG00000231252 (HGNC:):

ENSG00000231252 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000231252	ENST00000634701.1 link	n.60+3886C>T	intron_variant	Intron 1 of 9	5
ENSG00000231252	ENST00000635290.1 link	n.82+3886C>T	intron_variant	Intron 1 of 8	5
ENSG00000231252	ENST00000663928.1 link	n.64+3886C>T	intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.0502

AC:

7628

AN:

152024

Hom.:

260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0149

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0889

Gnomad ASJ

AF:

0.0637

Gnomad EAS

AF:

0.00269

Gnomad SAS

AF:

0.0297

Gnomad FIN

AF:

0.0341

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0703

Gnomad OTH

AF:

0.0543

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

GnomAD4 genome

AF:

0.0501

AC:

7625

AN:

152142

Hom.:

259

Cov.:

AF XY:

0.0486

AC XY:

3613

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0148

AC:

616

AN:

41510

American (AMR)

AF:

0.0889

AC:

1358

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0637

AC:

221

AN:

3470

East Asian (EAS)

AF:

0.00270

AC:

AN:

5184

South Asian (SAS)

AF:

0.0297

AC:

143

AN:

4812

European-Finnish (FIN)

AF:

0.0341

AC:

361

AN:

10574

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0702

AC:

4777

AN:

68002

Other (OTH)

AF:

0.0528

AC:

111

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

343

685

1028

1370

1713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0471

Hom.:

Bravo

AF:

0.0547

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

(source)

DANN

Benign

0.83

PhyloP100

-0.36

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