rs34555243

Variant names:

• chrY-12362246-G-C
• rs34555243
• ENST00000443820.2:n.65G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000443820.2(ARSDP1):​n.65G>C 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: ARSDP1 ENST00000443820.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 publications found

Genes affected

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

LOC107987343 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	n.1467C>G		non_coding_transcript_exon_variant	Exon 1 of 3
ARSDP1		n.12362246G>C		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000300 AC: 10 AN: 33292 Hom.: 0 Cov.: 0

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: 87 AN: 355421 Hom.: 0 Cov.: 0 AF XY: 0.000245 AC XY: 87 AN XY: 355421

African (AFR) AF: 0.00623 AC: 43 AN: 6897

American (AMR) AF: 0.00 AC: 0 AN: 9334

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6665

East Asian (EAS) AF: 0.00 AC: 0 AN: 9338

South Asian (SAS) AF: 0.00 AC: 0 AN: 31434

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12587

Middle Eastern (MID) AF: 0.00187 AC: 3 AN: 1608

European-Non Finnish (NFE) AF: 0.000114 AC: 30 AN: 263532

Other (OTH) AF: 0.000784 AC: 11 AN: 14026

GnomAD4 genome AF: 0.000360 AC: 12 AN: 33357 Hom.: 0 Cov.: 0 AF XY: 0.000360 AC XY: 12 AN XY: 33357

African (AFR) AF: 0.000932 AC: 8 AN: 8584

American (AMR) AF: 0.000277 AC: 1 AN: 3613

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 771

East Asian (EAS) AF: 0.00 AC: 0 AN: 1258

South Asian (SAS) AF: 0.00 AC: 0 AN: 1428

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3395

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.000221 AC: 3 AN: 13555

Other (OTH) AF: 0.00 AC: 0 AN: 468

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs34555243; hg19: chrY-14482977;