ENST00000671607.2:n.162-47839T>C

Variant names:

• chr5-44706396-A-G
• rs10941679
• ENST00000671607.2:n.162-47839T>C

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.162-47839T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,982 control chromosomes in the GnomAD database, including 5,365 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 0.25 (5365 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 165 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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.162-47839T>C		intron_variant	Intron 1 of 4
MRPS30-DT	ENST00000715752.1	n.411+38815T>C		intron_variant	Intron 3 of 6
MRPS30-DT	ENST00000715753.1	n.607+26497T>C		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38550 AN: 151864 Hom.: 5344 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.254 AC: 38596 AN: 151982 Hom.: 5365 Cov.: 32 AF XY: 0.260 AC XY: 19313 AN XY: 74278

African (AFR) AF: 0.189 AC: 7838 AN: 41506

American (AMR) AF: 0.341 AC: 5193 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2569 AN: 5146

South Asian (SAS) AF: 0.366 AC: 1762 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2681 AN: 10552

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17097 AN: 67938

Other (OTH) AF: 0.267 AC: 563 AN: 2108

Alfa AF: 0.257 Hom.: 10835

Bravo AF: 0.257

Asia WGS AF: 0.431 AC: 1497 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10941679; hg19: chr5-44706498;