chr15-96266553-A-G

Variant names:

• chr15-96266553-A-G
• rs1437588
• ENST00000560395.5:n.417T>C

Variant summary

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

The ENST00000560395.5(NR2F2-AS1):​n.417T>C variant causes a non coding transcript exon 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 ENST00000560395.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 6 publications found

Genes affected

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

ENSG00000275443 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NR2F2-AS1	NR_102743.1	n.983T>C		non_coding_transcript_exon_variant	Exon 8 of 8
NR2F2-AS1	NR_125738.1	n.317+24077T>C		intron_variant	Intron 2 of 4
LOC124903584	XR_007064801.1	n.8852-8430A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000560395.5	n.417T>C		non_coding_transcript_exon_variant	Exon 5 of 5	5
NR2F2-AS1	ENST00000561402.6	n.906T>C		non_coding_transcript_exon_variant	Exon 7 of 7	3
NR2F2-AS1	ENST00000690325.2	n.643T>C		non_coding_transcript_exon_variant	Exon 5 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.877 AC: 36393 AN: 41502

American (AMR) AF: 0.551 AC: 8410 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2078 AN: 5176

South Asian (SAS) AF: 0.575 AC: 2763 AN: 4808

European-Finnish (FIN) AF: 0.441 AC: 4639 AN: 10514

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36228 AN: 67974

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.565 Hom.: 31654

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1437588; hg19: chr15-96809782;