rs10491195

Positions:

• chr17-49520934-A-G

Variant summary

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

The NR_103773.1(NGFR-AS1):​n.247-9821T>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 0.0932 in 152,204 control chromosomes in the GnomAD database, including 800 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 0.093 (800 hom., cov: 32)
• Consequence: NGFR-AS1 NR_103773.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

NGFR-AS1 (HGNC:55555): (NGFR antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NGFR-AS1	NR_103773.1	n.247-9821T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NGFR-AS1	ENST00000514506.1	n.247-9821T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14189 AN: 152086 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0932 AC: 14183 AN: 152204 Hom.: 800 Cov.: 32 AF XY: 0.0932 AC XY: 6938 AN XY: 74410

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.103

Alfa AF: 0.119 Hom.: 1244

Bravo AF: 0.0915

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.092
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491195; hg19: chr17-47598296;