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 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
• 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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443820.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARSDP1	ENST00000443820.2	TSL:6	n.65G>C		non_coding_transcript_exon	Exon 2 of 10
	ENSG00000291034	ENST00000382966.5	TSL:3	n.284-7475C>G		intron	N/A
	ENSG00000291034	ENST00000651802.1		n.450+44138C>G		intron	N/A

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 v4.9

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;