3-185968952-A-G

Variant names:

• chr3-185968952-A-G
• rs10049246
• ENST00000416764.5:n.349+235A>G

Variant summary

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

The ENST00000416764.5(NMRAL2P):​n.349+235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 151,938 control chromosomes in the GnomAD database, including 35,012 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 0.67 (35012 hom., cov: 31)
• Consequence: NMRAL2P ENST00000416764.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 15 publications found

Genes affected

NMRAL2P (HGNC:):

NMRAL2P (HGNC:52332): (NmrA like redox sensor 2, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416764.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMRAL2P	NR_151491.1		n.137-2663A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMRAL2P	ENST00000416764.5	TSL:1	n.349+235A>G		intron	N/A
	NMRAL2P	ENST00000824373.1		n.819A>G		non_coding_transcript_exon	Exon 2 of 2
	NMRAL2P	ENST00000306399.3	TSL:6	n.270+244A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101729 AN: 151822 Hom.: 34959 Cov.: 31

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.670 AC: 101840 AN: 151938 Hom.: 35012 Cov.: 31 AF XY: 0.676 AC XY: 50187 AN XY: 74272

African (AFR) AF: 0.809 AC: 33509 AN: 41430

American (AMR) AF: 0.724 AC: 11044 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2474 AN: 3472

East Asian (EAS) AF: 0.761 AC: 3928 AN: 5162

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4820

European-Finnish (FIN) AF: 0.608 AC: 6415 AN: 10548

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38679 AN: 67940

Other (OTH) AF: 0.677 AC: 1429 AN: 2112

Alfa AF: 0.606 Hom.: 121790

Bravo AF: 0.679

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0070
DANN	Benign	0.42
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10049246; hg19: chr3-185686741;