chr5-44714228-T-C

Variant names:

• chr5-44714228-T-C
• rs2218080
• ENST00000671607.2:n.162-55671A>G

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.162-55671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,906 control chromosomes in the GnomAD database, including 20,625 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 0.50 (20625 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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.162-55671A>G		intron_variant	Intron 1 of 4
MRPS30-DT	ENST00000715752.1	n.411+30983A>G		intron_variant	Intron 3 of 6
MRPS30-DT	ENST00000715753.1	n.607+18665A>G		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76418 AN: 151788 Hom.: 20575 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.504 AC: 76527 AN: 151906 Hom.: 20625 Cov.: 32 AF XY: 0.506 AC XY: 37534 AN XY: 74224

African (AFR) AF: 0.701 AC: 29065 AN: 41450

American (AMR) AF: 0.487 AC: 7408 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1491 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2869 AN: 5158

South Asian (SAS) AF: 0.492 AC: 2366 AN: 4808

European-Finnish (FIN) AF: 0.396 AC: 4174 AN: 10550

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27710 AN: 67938

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.414 Hom.: 10214

Bravo AF: 0.520

Asia WGS AF: 0.568 AC: 1967 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.6
DANN	Benign	0.61
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs2218080; hg19: chr5-44714330;