Genetic Variant ENSG00000285216:n.560+62974T>C (chr6-8370534-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000644718.1(ENSG00000285216):n.560+62974T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 148,170 control chromosomes in the GnomAD database, including 4,253 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 0.24 ( 4253 hom., cov: 27)

Consequence

ENSG00000285216
ENST00000644718.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

Publications

3 publications found

Variant links:

Genes affected

ENSG00000285216 (HGNC:):

ENSG00000285216 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=-1.1).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285216	ENST00000644718.1 link	n.560+62974T>C	intron_variant	Intron 5 of 8
ENSG00000234763	ENST00000651914.1 link	n.160-2118A>G	intron_variant	Intron 2 of 4
ENSG00000234763	ENST00000655767.2 link	n.262-7702A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

35247

AN:

148080

Hom.:

4251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.0932

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.235

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.238

AC:

35266

AN:

148170

Hom.:

4253

Cov.:

AF XY:

0.232

AC XY:

16738

AN XY:

72018

show subpopulations

African (AFR)

AF:

0.213

AC:

8475

AN:

39704

American (AMR)

AF:

0.244

AC:

3564

AN:

14590

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

973

AN:

3464

East Asian (EAS)

AF:

0.0930

AC:

458

AN:

4926

South Asian (SAS)

AF:

0.213

AC:

1000

AN:

4696

European-Finnish (FIN)

AF:

0.210

AC:

2073

AN:

9874

Middle Eastern (MID)

AF:

0.227

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.267

AC:

18033

AN:

67662

Other (OTH)

AF:

0.251

AC:

520

AN:

2068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.534

Heterozygous variant carriers

1323

2646

3970

5293

6616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.250

Hom.:

635

Bravo

AF:

0.236

Asia WGS

AF:

0.144

AC:

504

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.12

(source)

DANN

Benign

0.15

PhyloP100

-1.9

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