dbSNP rs2844573: ENSG00000285647:n.1588A>C (chr6-31367677-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755531.1(ENSG00000285647):n.1588A>C 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 0.212 in 152,220 control chromosomes in the GnomAD database, including 4,244 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 0.21 ( 4244 hom., cov: 33)

Consequence

ENSG00000285647
ENST00000755531.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.645

Publications

16 publications found

Variant links:

Genes affected

ENSG00000285647 (HGNC:):

ENSG00000285647 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285647	ENST00000755531.1 link	n.1588A>C	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285647	ENST00000649421.2 link	n.274+347A>C	intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1 link	n.326+13480A>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32325

AN:

152102

Hom.:

4247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0958

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.212

AC:

32327

AN:

152220

Hom.:

4244

Cov.:

AF XY:

0.205

AC XY:

15245

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0957

AC:

3975

AN:

41554

American (AMR)

AF:

0.129

AC:

1974

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.104

AC:

361

AN:

3468

East Asian (EAS)

AF:

0.186

AC:

965

AN:

5186

South Asian (SAS)

AF:

0.124

AC:

600

AN:

4830

European-Finnish (FIN)

AF:

0.264

AC:

2796

AN:

10586

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.308

AC:

20935

AN:

67982

Other (OTH)

AF:

0.169

AC:

357

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1225

2450

3675

4900

6125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.236

Hom.:

5505

Bravo

AF:

0.196

Asia WGS

AF:

0.160

AC:

557

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.65

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