5-44708276-C-G

Variant names:

• chr5-44708276-C-G
• rs6861560
• ENST00000671607.2:n.162-49719G>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.162-49719G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,616 control chromosomes in the GnomAD database, including 18,404 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 0.48 (18404 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671607.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000671607.2		n.162-49719G>C		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.411+36935G>C		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.607+24617G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72919 AN: 151496 Hom.: 18352 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.482 AC: 73023 AN: 151616 Hom.: 18404 Cov.: 32 AF XY: 0.486 AC XY: 35974 AN XY: 74056

African (AFR) AF: 0.624 AC: 25816 AN: 41368

American (AMR) AF: 0.497 AC: 7567 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1506 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2880 AN: 5114

South Asian (SAS) AF: 0.509 AC: 2450 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4196 AN: 10430

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27190 AN: 67880

Other (OTH) AF: 0.466 AC: 982 AN: 2108

Alfa AF: 0.286 Hom.: 651

Bravo AF: 0.496

Asia WGS AF: 0.572 AC: 1981 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.33
PhyloP100		-0.73

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6861560;

hg19: chr5-44708378;