chr5-53122752-G-A

Variant names:

• chr5-53122752-G-A
• rs30099
• ENST00000660072.1:n.1336-327G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660072.1(MOCS2-DT):​n.1336-327G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOCS2-DT	ENST00000660072.1	n.1336-327G>A		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.154 AC: 6374 AN: 41450

American (AMR) AF: 0.0697 AC: 1064 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2178 AN: 5158

South Asian (SAS) AF: 0.174 AC: 837 AN: 4818

European-Finnish (FIN) AF: 0.0721 AC: 763 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6168 AN: 67988

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Alfa AF: 0.0974 Hom.: 1348

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
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs30099; hg19: chr5-52418582;