6-44126005-C-T

Position:

• chr6-44126005-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032111.4(MRPL14):​c.-19+1339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,066 control chromosomes in the GnomAD database, including 29,659 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.61 (29659 hom., cov: 33)
• Consequence: MRPL14 NM_032111.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.40

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]

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 6-44126005-C-T is Benign according to our data. Variant chr6-44126005-C-T is described in ClinVar as [Benign]. Clinvar id is 2786327.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPL14	NM_032111.4	c.-19+1339G>A		intron_variant		ENST00000372014.5	NP_115487.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL14	ENST00000372014.5	c.-19+1339G>A		intron_variant		1	NM_032111.4	ENSP00000361084	P1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92699 AN: 151948 Hom.: 29615 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.610 AC: 92805 AN: 152066 Hom.: 29659 Cov.: 33 AF XY: 0.612 AC XY: 45511 AN XY: 74326

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.623

Alfa AF: 0.533 Hom.: 6826

Bravo AF: 0.636

Asia WGS AF: 0.647 AC: 2250 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.89

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935611; hg19: chr6-44093742;