6-44124392-T-G

Variant names:

• chr6-44124392-T-G
• rs713050
• NM_032111.4:c.-19+2952A>C

Variant summary

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

The NM_032111.4(MRPL14):​c.-19+2952A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,178 control chromosomes in the GnomAD database, including 1,637 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 0.14 (1637 hom., cov: 32)
• Consequence: MRPL14 NM_032111.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 7 publications found

Genes affected

MRPL14 (HGNC:14279): (mitochondrial ribosomal protein L14) This nuclear gene encodes a protein component of the 39S subunit of the mitochondrial ribosome. A pseudogene of this gene is found on chromosome 17. [provided by RefSeq, Jan 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL14	NM_032111.4	c.-19+2952A>C		intron_variant	Intron 1 of 2	ENST00000372014.5	NP_115487.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL14	ENST00000372014.5	c.-19+2952A>C		intron_variant	Intron 1 of 2	1	NM_032111.4	ENSP00000361084.3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21412 AN: 152062 Hom.: 1638 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.141 AC: 21424 AN: 152178 Hom.: 1637 Cov.: 32 AF XY: 0.139 AC XY: 10311 AN XY: 74412

African (AFR) AF: 0.153 AC: 6342 AN: 41480

American (AMR) AF: 0.196 AC: 2995 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.0571 AC: 296 AN: 5180

South Asian (SAS) AF: 0.113 AC: 543 AN: 4824

European-Finnish (FIN) AF: 0.0748 AC: 794 AN: 10610

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9449 AN: 67996

Other (OTH) AF: 0.157 AC: 331 AN: 2110

Alfa AF: 0.129 Hom.: 983

Bravo AF: 0.153

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.66
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs713050; hg19: chr6-44092129;