dbSNP rs9465673: ENSG00000227803:n.91+38418G>A (chr6-20250595-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 ENST00000449143.2(ENSG00000227803):n.91+38418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,112 control chromosomes in the GnomAD database, including 3,039 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 0.20 ( 3039 hom., cov: 32)

Consequence

ENSG00000227803
ENST00000449143.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

1 publications found

Variant links:

Genes affected

ENSG00000227803 (HGNC:):

ENSG00000227803 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 (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000227803	ENST00000449143.2 link	n.91+38418G>A	intron_variant	Intron 1 of 2	3
ENSG00000227803	ENST00000718207.1 link	n.81-15128G>A	intron_variant	Intron 1 of 4
ENSG00000227803	ENST00000718208.1 link	n.59-29456G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29718

AN:

151994

Hom.:

3036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.0919

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.195

AC:

29726

AN:

152112

Hom.:

3039

Cov.:

AF XY:

0.201

AC XY:

14909

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.171

AC:

7086

AN:

41498

American (AMR)

AF:

0.154

AC:

2355

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

711

AN:

3470

East Asian (EAS)

AF:

0.0919

AC:

476

AN:

5180

South Asian (SAS)

AF:

0.275

AC:

1326

AN:

4820

European-Finnish (FIN)

AF:

0.287

AC:

3029

AN:

10560

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.207

AC:

14099

AN:

67990

Other (OTH)

AF:

0.191

AC:

402

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1198

2396

3594

4792

5990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.202

Hom.:

5261

Bravo

AF:

0.180

Asia WGS

AF:

0.171

AC:

593

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

2.7

(source)

DANN

Benign

0.64

PhyloP100

0.35

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