dbSNP rs1340044: ENSG00000227167:n.114A>T (chr9-18362107-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000443359.1(ENSG00000227167):n.114A>T 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 0.525 in 151,908 control chromosomes in the GnomAD database, including 20,983 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 0.52 ( 20980 hom., cov: 32)

Exomes 𝑓: 0.80 ( 3 hom. )

Consequence

ENSG00000227167
ENST00000443359.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Publications

5 publications found

Variant links:

Genes affected

ENSG00000227167 (HGNC:):

ENSG00000227167 links:

ADAMTSL1 (HGNC:14632): (ADAMTS like 1) This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]

ADAMTSL1 links:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
LOC107986990	XR_001746428.1 link	n.9316T>A	non_coding_transcript_exon_variant	Exon 2 of 3
ADAMTSL1	XM_011518063.3 link	c.262-142722T>A	intron_variant	Intron 3 of 30	XP_011516365.1
ADAMTSL1	XM_017015310.2 link	c.220-142722T>A	intron_variant	Intron 2 of 29	XP_016870799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227167	ENST00000443359.1 link	n.114A>T		non_coding_transcript_exon_variant	Exon 1 of 2	5
ADAMTSL1	ENST00000680146.1 link	c.208-142722T>A		intron_variant	Intron 2 of 29			ENSP00000505591.1		A0A7P0T9B9

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79617

AN:

151780

Hom.:

20963

Cov.:

show subpopulations

Gnomad AFR

AF:

0.534

Gnomad AMI

AF:

0.539

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.504

Gnomad FIN

AF:

0.518

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.510

GnomAD4 exome

AF:

0.800

AC:

AN:

Hom.:

Cov.:

AF XY:

0.800

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.524

AC:

79668

AN:

151898

Hom.:

20980

Cov.:

AF XY:

0.520

AC XY:

38579

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.534

AC:

22120

AN:

41400

American (AMR)

AF:

0.437

AC:

6675

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1733

AN:

3468

East Asian (EAS)

AF:

0.593

AC:

3055

AN:

5156

South Asian (SAS)

AF:

0.504

AC:

2423

AN:

4810

European-Finnish (FIN)

AF:

0.518

AC:

5468

AN:

10548

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.537

AC:

36484

AN:

67932

Other (OTH)

AF:

0.512

AC:

1083

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1938

3875

5813

7750

9688

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<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:

0.520

Hom.:

2551

Bravo

AF:

0.518

Asia WGS

AF:

0.518

AC:

1802

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.15

(source)

DANN

Benign

0.54

PhyloP100

-1.2

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