Genetic Variant ENSG00000287877:n.270-10915A>T (chr6-165065309-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000667740.1(ENSG00000287877):n.270-10915A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 148,890 control chromosomes in the GnomAD database, including 2,846 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 0.18 ( 2846 hom., cov: 32)

Consequence

ENSG00000287877
ENST00000667740.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.818

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287877 (HGNC:):

ENSG00000287877 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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287877	ENST00000667740.1 link	n.270-10915A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

26942

AN:

148774

Hom.:

2834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.197

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

GnomAD4 genome

AF:

0.181

AC:

26992

AN:

148890

Hom.:

2846

Cov.:

AF XY:

0.183

AC XY:

13287

AN XY:

72792

show subpopulations

African (AFR)

AF:

0.236

AC:

9383

AN:

39786

American (AMR)

AF:

0.178

AC:

2627

AN:

14788

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

484

AN:

3412

East Asian (EAS)

AF:

0.464

AC:

2352

AN:

5066

South Asian (SAS)

AF:

0.209

AC:

973

AN:

4660

European-Finnish (FIN)

AF:

0.112

AC:

1176

AN:

10544

Middle Eastern (MID)

AF:

0.157

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.138

AC:

9309

AN:

67398

Other (OTH)

AF:

0.201

AC:

410

AN:

2044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1085

2169

3254

4338

5423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.168

Hom.:

244

Asia WGS

AF:

0.336

AC:

1166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.25

PhyloP100

-0.82

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