dbSNP rs9469003: ENSG00000288587:n.63-23072T>C (chr6-31440051-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 ENST00000673857.1(ENSG00000288587):n.63-23072T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,732 control chromosomes in the GnomAD database, including 4,229 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 0.22 ( 4229 hom., cov: 32)

Consequence

ENSG00000288587
ENST00000673857.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.965

Publications

57 publications found

Variant links:

Genes affected

ENSG00000288587 (HGNC:):

ENSG00000288587 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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
ENSG00000288587	ENST00000673857.1 link	n.63-23072T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32747

AN:

151614

Hom.:

4221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.216

AC:

32792

AN:

151732

Hom.:

4229

Cov.:

AF XY:

0.221

AC XY:

16402

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.313

AC:

12906

AN:

41204

American (AMR)

AF:

0.268

AC:

4079

AN:

15198

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

955

AN:

3468

East Asian (EAS)

AF:

0.173

AC:

894

AN:

5170

South Asian (SAS)

AF:

0.227

AC:

1091

AN:

4808

European-Finnish (FIN)

AF:

0.233

AC:

2461

AN:

10570

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.141

AC:

9591

AN:

68000

Other (OTH)

AF:

0.203

AC:

429

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1235

2470

3704

4939

6174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<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.:

8121

Bravo

AF:

0.222

Asia WGS

AF:

0.197

AC:

684

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.9

(source)

DANN

Benign

0.42

PhyloP100

-0.96

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