6-18407512-T-C

Variant names:

• chr6-18407512-T-C
• rs1408263
• NM_182757.4:c.165+7813T>C

Variant summary

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

The NM_182757.4(RNF144B):​c.165+7813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,048 control chromosomes in the GnomAD database, including 31,818 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 0.64 (31818 hom., cov: 32)
• Consequence: RNF144B NM_182757.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 6 publications found

Genes affected

RNF144B (HGNC:21578): (ring finger protein 144B) Enables ubiquitin-protein transferase activity. Involved in negative regulation of apoptotic process and ubiquitin-dependent protein catabolic process. Located in mitochondrial membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF144B	NM_182757.4	c.165+7813T>C		intron_variant	Intron 2 of 7	ENST00000259939.4	NP_877434.2
RNF144B	XM_047418594.1	c.165+7813T>C		intron_variant	Intron 1 of 5		XP_047274550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF144B	ENST00000259939.4	c.165+7813T>C		intron_variant	Intron 2 of 7	1	NM_182757.4	ENSP00000259939.4

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97893 AN: 151928 Hom.: 31810 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.644 AC: 97948 AN: 152048 Hom.: 31818 Cov.: 32 AF XY: 0.639 AC XY: 47492 AN XY: 74330

African (AFR) AF: 0.584 AC: 24182 AN: 41428

American (AMR) AF: 0.613 AC: 9365 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3508 AN: 5182

South Asian (SAS) AF: 0.589 AC: 2841 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6158 AN: 10554

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47212 AN: 67988

Other (OTH) AF: 0.669 AC: 1412 AN: 2112

Alfa AF: 0.674 Hom.: 108575

Bravo AF: 0.644

Asia WGS AF: 0.646 AC: 2244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.78
PhyloP100		-0.29
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: rs1408263; hg19: chr6-18407743;