dbSNP rs34555243: ARSDP1:n.65G>C (chrY-12362246-G-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The XR_001756060.1(LOC107987343):n.1467C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.00036 ( 0 hom., 12 hem., cov: 0)

Exomes 𝑓: 0.00024 ( 0 hom. 87 hem. )

Failed GnomAD Quality Control

Consequence

LOC107987343
XR_001756060.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

ARSDP1 (HGNC:718): (arylsulfatase D pseudogene 1)

ARSDP1 links:

LOC107987343 (HGNC:):

LOC107987343 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BS2

High Hemizygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987343	XR_001756060.1 link	n.1467C>G		non_coding_transcript_exon_variant	Exon 1 of 3
ARSDP1		n.12362246G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ARSDP1	ENST00000443820.2 link	n.65G>C	non_coding_transcript_exon_variant	Exon 2 of 10	6
ENSG00000291034	ENST00000382966.5 link	n.284-7475C>G	intron_variant	Intron 2 of 2	3
ENSG00000291034	ENST00000651802.1 link	n.450+44138C>G	intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes

AF:

0.000300

AC:

AN:

33292

Hom.:

Cov.:

AF XY:

0.000300

AC XY:

AN XY:

33292

show subpopulations

Gnomad AFR

AF:

0.000703

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000277

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000245

AC:

AN:

355421

Hom.:

Cov.:

AF XY:

0.000245

AC XY:

AN XY:

355421

show subpopulations

Gnomad4 AFR exome

AF:

0.00623

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000114

Gnomad4 OTH exome

AF:

0.000784

GnomAD4 genome

AF:

0.000360

AC:

AN:

33357

Hom.:

Cov.:

AF XY:

0.000360

AC XY:

AN XY:

33357

show subpopulations

Gnomad4 AFR

AF:

0.000932

Gnomad4 AMR

AF:

0.000277

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.7

DANN

Benign

0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over