rs30099

Positions:

• chr5-53122752-G-A

Variant summary

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

The ENST00000660072.1(MOCS2-DT):​n.1336-327G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,050 control chromosomes in the GnomAD database, including 1,487 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 0.12 (1487 hom., cov: 32)
• Consequence: MOCS2-DT ENST00000660072.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

MOCS2-DT (HGNC:27417): (MOCS2 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOCS2-DT	ENST00000660072.1	n.1336-327G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17887 AN: 151932 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.118 AC: 17909 AN: 152050 Hom.: 1487 Cov.: 32 AF XY: 0.121 AC XY: 8961 AN XY: 74342

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.0907

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0963 Hom.: 1043

Bravo AF: 0.120

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30099; hg19: chr5-52418582;