dbSNP rs12443880: ENSG00000260249:n.4340T>G (chr16-50670764-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000570241.3(ENSG00000260249):n.4340T>G 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 0.0831 in 152,272 control chromosomes in the GnomAD database, including 1,399 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 0.083 ( 1398 hom., cov: 32)

Exomes 𝑓: 0.059 ( 1 hom. )

Consequence

ENSG00000260249
ENST00000570241.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

Publications

4 publications found

Variant links:

Genes affected

ENSG00000260249 (HGNC:):

ENSG00000260249 links:

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
LOC101927272	NR_110908.1 link	n.388T>G	non_coding_transcript_exon_variant	Exon 2 of 3
SNX20	NM_153337.3 link	c.283-1616A>C	intron_variant	Intron 3 of 3	NP_699168.1	Q7Z614-3
SNX20	NM_001144972.2 link	c.283-2723A>C	intron_variant	Intron 3 of 3	NP_001138444.1	Q7Z614-4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000260249	ENST00000570241.3 link	n.4340T>G	non_coding_transcript_exon_variant	Exon 2 of 3	1
SNX20	ENST00000423026.6 link	c.283-2723A>C	intron_variant	Intron 3 of 3	1	ENSP00000388875.2	Q7Z614-4
SNX20	ENST00000568993.5 link	n.283-1616A>C	intron_variant	Intron 3 of 4	1	ENSP00000454863.1	Q7Z614-3

Frequencies

GnomAD3 genomes

AF:

0.0827

AC:

12585

AN:

152086

Hom.:

1385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.0110

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00501

Gnomad OTH

AF:

0.0559

GnomAD4 exome

AF:

0.0588

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0652

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0217

AC:

AN:

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0831

AC:

12651

AN:

152204

Hom.:

1398

Cov.:

AF XY:

0.0821

AC XY:

6112

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.251

AC:

10431

AN:

41488

American (AMR)

AF:

0.0621

AC:

950

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0159

AC:

AN:

3468

East Asian (EAS)

AF:

0.112

AC:

581

AN:

5172

South Asian (SAS)

AF:

0.0104

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0107

AC:

114

AN:

10612

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00501

AC:

341

AN:

68016

Other (OTH)

AF:

0.0563

AC:

119

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

519

1038

1558

2077

2596

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0339

Hom.:

628

Bravo

AF:

0.0942

Asia WGS

AF:

0.0740

AC:

255

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.0

(source)

DANN

Benign

0.81

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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