dbSNP rs6588761: ENSG00000296622:n.1256G>A (chr10-47139553-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 ENST00000740894.1(ENSG00000296622):n.1256G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 151,968 control chromosomes in the GnomAD database, including 1,255 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 0.085 ( 1255 hom., cov: 30)

Consequence

ENSG00000296622
ENST00000740894.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.990

Publications

1 publications found

Variant links:

Genes affected

ENSG00000296622 (HGNC:):

ENSG00000296622 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296622	ENST00000740894.1 link	n.1256G>A	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296622	ENST00000740895.1 link	n.391G>A	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296622	ENST00000740878.1 link	n.380+1397G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0846

AC:

12850

AN:

151850

Hom.:

1251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0542

Gnomad ASJ

AF:

0.0985

Gnomad EAS

AF:

0.000966

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.00547

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0222

Gnomad OTH

AF:

0.0844

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

GnomAD4 genome

AF:

0.0848

AC:

12880

AN:

151968

Hom.:

1255

Cov.:

AF XY:

0.0814

AC XY:

6049

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.239

AC:

9869

AN:

41324

American (AMR)

AF:

0.0540

AC:

826

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0985

AC:

341

AN:

3462

East Asian (EAS)

AF:

0.000968

AC:

AN:

5164

South Asian (SAS)

AF:

0.0123

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00547

AC:

AN:

10602

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0222

AC:

1507

AN:

68002

Other (OTH)

AF:

0.0835

AC:

176

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

530

1060

1591

2121

2651

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0661

Hom.:

117

Bravo

AF:

0.0965

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

-0.91

CADD

Benign

1.0

(source)

DANN

Benign

0.83

PhyloP100

-0.99

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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