rs10049246

Positions:

• chr3-185968952-A-G
• chr3-185968952-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_151491.1(NMRAL2P):​n.137-2663A>G variant causes a intron, non coding transcript 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 NR_151491.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NMRAL2P	NR_151491.1	n.137-2663A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NMRAL2P	ENST00000306399.3	n.270+244A>G		intron_variant, non_coding_transcript_variant
NMRAL2P	ENST00000423298.5	n.137-2663A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.677

Alfa AF: 0.598 Hom.: 52643

Bravo AF: 0.679

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10049246; hg19: chr3-185686741;