rs1437588

Positions:

• chr15-96266553-A-G
• chr15-96266553-A-T

Variant summary

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

The NR_125738.1(NR2F2-AS1):​n.317+24077T>C 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 0.621 in 152,030 control chromosomes in the GnomAD database, including 31,438 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 0.62 (31438 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: NR2F2-AS1 NR_125738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

NR2F2-AS1 (HGNC:44222): (NR2F2 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR2F2-AS1	NR_125738.1	n.317+24077T>C		intron_variant, non_coding_transcript_variant
LOC124903584	XR_007064801.1	n.8852-8430A>G		intron_variant, non_coding_transcript_variant
NR2F2-AS1	NR_102743.1	n.983T>C		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR2F2-AS1	ENST00000560800.5	n.220+24077T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000619812.1	n.454+14348A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94351 AN: 151912 Hom.: 31393 Cov.: 33

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.611

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.621 AC: 94455 AN: 152030 Hom.: 31438 Cov.: 33 AF XY: 0.615 AC XY: 45705 AN XY: 74288

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.608

Alfa AF: 0.553 Hom.: 22830

Bravo AF: 0.635

Asia WGS AF: 0.501 AC: 1737 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437588; hg19: chr15-96809782;