Genetic Variant ENSG00000306704:n.264+54815T>C (chr6-87840077-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 ENST00000820282.1(ENSG00000306704):n.264+54815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,136 control chromosomes in the GnomAD database, including 6,943 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 0.29 ( 6943 hom., cov: 32)

Consequence

ENSG00000306704
ENST00000820282.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64

Publications

2 publications found

Variant links:

Genes affected

ENSG00000306704 (HGNC:):

ENSG00000306704 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928911	NR_110869.1 link	n.260+54815T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000306704	ENST00000820282.1 link	n.264+54815T>C	intron_variant	Intron 1 of 4
ENSG00000306704	ENST00000820283.1 link	n.287+54815T>C	intron_variant	Intron 1 of 1
ENSG00000306704	ENST00000820284.1 link	n.273-25369T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43717

AN:

152018

Hom.:

6941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.264

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

GnomAD4 genome

AF:

0.288

AC:

43753

AN:

152136

Hom.:

6943

Cov.:

AF XY:

0.286

AC XY:

21245

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.435

AC:

18023

AN:

41450

American (AMR)

AF:

0.268

AC:

4099

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

980

AN:

3468

East Asian (EAS)

AF:

0.222

AC:

1146

AN:

5166

South Asian (SAS)

AF:

0.225

AC:

1085

AN:

4826

European-Finnish (FIN)

AF:

0.205

AC:

2170

AN:

10590

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.226

AC:

15400

AN:

68018

Other (OTH)

AF:

0.264

AC:

559

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1533

3066

4598

6131

7664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.248

Hom.:

20001

Bravo

AF:

0.300

Asia WGS

AF:

0.255

AC:

886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

1.6

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