5-44627903-C-T

Variant names:

• chr5-44627903-C-T
• rs12652273
• ENST00000671607.2:n.257+30559G>A

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.257+30559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,490 control chromosomes in the GnomAD database, including 2,958 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 0.18 (2958 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 1 publications found

Genes affected

MRPS30-DT (HGNC:53420): (MRPS30 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
MRPS30-DT	ENST00000671607.2	n.257+30559G>A		intron_variant	Intron 2 of 4
MRPS30-DT	ENST00000715752.1	n.1088+30559G>A		intron_variant	Intron 4 of 6
MRPS30-DT	ENST00000715753.1	n.703+30559G>A		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27124 AN: 151372 Hom.: 2951 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.179 AC: 27154 AN: 151490 Hom.: 2958 Cov.: 32 AF XY: 0.178 AC XY: 13183 AN XY: 74042

African (AFR) AF: 0.312 AC: 12865 AN: 41262

American (AMR) AF: 0.138 AC: 2093 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3466

East Asian (EAS) AF: 0.132 AC: 678 AN: 5148

South Asian (SAS) AF: 0.121 AC: 581 AN: 4806

European-Finnish (FIN) AF: 0.111 AC: 1164 AN: 10454

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.125 AC: 8507 AN: 67856

Other (OTH) AF: 0.163 AC: 343 AN: 2106

Alfa AF: 0.0709 Hom.: 82

Bravo AF: 0.189

Asia WGS AF: 0.134 AC: 463 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs12652273; hg19: chr5-44628005;