dbSNP rs77693245: ENSG00000287294:n.185+2667G>A (chr6-84765153-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 ENST00000790820.1(ENSG00000287294):n.185+2667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0495 in 152,216 control chromosomes in the GnomAD database, including 223 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 ( 223 hom., cov: 33)

Consequence

ENSG00000287294
ENST00000790820.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.842

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287294 (HGNC:):

ENSG00000287294 links:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901353	XR_007059666.1 link	n.146+2667G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287294	ENST00000790820.1 link	n.185+2667G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0495

AC:

7522

AN:

152098

Hom.:

223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0755

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.0454

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0313

Gnomad FIN

AF:

0.0208

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0418

Gnomad OTH

AF:

0.0627

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

GnomAD4 genome

AF:

0.0495

AC:

7538

AN:

152216

Hom.:

223

Cov.:

AF XY:

0.0480

AC XY:

3573

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0757

AC:

3144

AN:

41518

American (AMR)

AF:

0.0453

AC:

693

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0444

AC:

154

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.0313

AC:

151

AN:

4824

European-Finnish (FIN)

AF:

0.0208

AC:

220

AN:

10598

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0418

AC:

2844

AN:

68018

Other (OTH)

AF:

0.0625

AC:

132

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

355

710

1065

1420

1775

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0394

Hom.:

226

Bravo

AF:

0.0527

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

-0.83

CADD

Benign

8.2

(source)

DANN

Benign

0.74

PhyloP100

0.84

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