rs10491195

Variant names:

• chr17-49520934-A-G
• rs10491195
• ENST00000514506.1:n.247-9821T>C

Variant summary

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

The ENST00000514506.1(NGFR-AS1):​n.247-9821T>C variant causes a intron 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 ENST00000514506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 5 publications found

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NGFR-AS1	NR_103773.1	n.247-9821T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NGFR-AS1	ENST00000514506.1	n.247-9821T>C		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.0334 AC: 1386 AN: 41540

American (AMR) AF: 0.0958 AC: 1464 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3472

East Asian (EAS) AF: 0.167 AC: 863 AN: 5182

South Asian (SAS) AF: 0.0479 AC: 231 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10598

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.116 AC: 7913 AN: 67988

Other (OTH) AF: 0.103 AC: 217 AN: 2116

Alfa AF: 0.115 Hom.: 1906

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10491195; hg19: chr17-47598296;