5-150299700-T-C

Position:

• chr5-150299700-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012301.4(ARSI):​c.312-1088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 151,782 control chromosomes in the GnomAD database, including 48,771 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 0.80 (48771 hom., cov: 29)
• Consequence: ARSI NM_001012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

ARSI (HGNC:32521): (arylsulfatase family member I) This gene encodes a protein that belongs to a large family of sulfatases that hydrolyze sulfate esters and sulfamates. Members of this family play a role in several cellular processes, including hormone synthesis, cell signaling in development and degradation of macromolecules. The protein encoded by this gene is thought to be secreted, and to function in extracellular space. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARSI	NM_001012301.4	c.312-1088A>G		intron_variant		ENST00000328668.8	NP_001012301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARSI	ENST00000328668.8	c.312-1088A>G		intron_variant		1	NM_001012301.4	ENSP00000333395.7
ARSI	ENST00000515301.2	c.-118-1088A>G		intron_variant		4		ENSP00000426879.2
ARSI	ENST00000509146.1	c.-118-1088A>G		intron_variant		4		ENSP00000420955.1

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120686 AN: 151664 Hom.: 48766 Cov.: 29

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.788

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.795 AC: 120727 AN: 151782 Hom.: 48771 Cov.: 29 AF XY: 0.793 AC XY: 58826 AN XY: 74158

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.790

Alfa AF: 0.826 Hom.: 6608

Bravo AF: 0.775

Asia WGS AF: 0.821 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9324643; hg19: chr5-149679263;