dbSNP rs2287195: SNX20:c.-10+122A>G (chr16-50681068-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 NM_182854.4(SNX20):c.-10+122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,290 control chromosomes in the GnomAD database, including 40,920 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 0.72 ( 40872 hom., cov: 32)

Exomes 𝑓: 0.73 ( 48 hom. )

Consequence

SNX20
NM_182854.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

18 publications found

Variant links:

Genes affected

SNX20 (HGNC:30390): (sorting nexin 20) SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]

SNX20 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 = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_182854.4 link	c.-10+122A>G	intron_variant	Intron 1 of 3	ENST00000330943.9	NP_878274.1	Q7Z614-1
SNX20	NM_153337.3 link	c.-10+122A>G	intron_variant	Intron 1 of 3		NP_699168.1	Q7Z614-3
SNX20	NM_001144972.2 link	c.-10+122A>G	intron_variant	Intron 1 of 3		NP_001138444.1	Q7Z614-4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNX20	ENST00000330943.9 link	c.-10+122A>G	intron_variant	Intron 1 of 3	1	NM_182854.4	ENSP00000332062.4	Q7Z614-1
SNX20	ENST00000423026.6 link	c.-10+122A>G	intron_variant	Intron 1 of 3	1		ENSP00000388875.2	Q7Z614-4
SNX20	ENST00000568993.5 link	n.-10+122A>G	intron_variant	Intron 1 of 4	1		ENSP00000454863.1	Q7Z614-3
SNX20	ENST00000300590.7 link	c.-10+122A>G	intron_variant	Intron 1 of 3	2		ENSP00000300590.3	Q7Z614-3

Frequencies

GnomAD3 genomes

AF:

0.721

AC:

109554

AN:

151990

Hom.:

40832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.753

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.825

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.703

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.701

GnomAD4 exome

AF:

0.731

AC:

133

AN:

182

Hom.:

AF XY:

0.700

AC XY:

AN XY:

120

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.728

AC:

AN:

136

Other (OTH)

AF:

0.688

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.556

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.721

AC:

109648

AN:

152108

Hom.:

40872

Cov.:

AF XY:

0.711

AC XY:

52832

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.821

AC:

34049

AN:

41484

American (AMR)

AF:

0.633

AC:

9674

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.825

AC:

2865

AN:

3472

East Asian (EAS)

AF:

0.255

AC:

1316

AN:

5160

South Asian (SAS)

AF:

0.384

AC:

1849

AN:

4820

European-Finnish (FIN)

AF:

0.703

AC:

7447

AN:

10590

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.737

AC:

50083

AN:

67972

Other (OTH)

AF:

0.696

AC:

1471

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1471

2943

4414

5886

7357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

812

1624

2436

3248

4060

<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:

0.718

Hom.:

9178

Bravo

AF:

0.721

Asia WGS

AF:

0.342

AC:

1193

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

0.25

(source)

DANN

Benign

0.40

PhyloP100

-1.3

PromoterAI

0.055

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over