rs296648

Positions:

• chr9-91066737-G-A
• chr9-91066737-G-C

Variant summary

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

The NR_033912.1(LOC100129316):​n.1918C>T 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 0.0569 in 152,204 control chromosomes in the GnomAD database, including 318 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 0.057 (318 hom., cov: 33)
• Consequence: LOC100129316 NR_033912.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

LOC100129316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100129316	NR_033912.1	n.1918C>T		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8667 AN: 152086 Hom.: 318 Cov.: 33

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0569 AC: 8666 AN: 152204 Hom.: 318 Cov.: 33 AF XY: 0.0582 AC XY: 4335 AN XY: 74432

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0498

Gnomad4 EAS AF: 0.0589

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0390 Hom.: 187

Bravo AF: 0.0554

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs296648; hg19: chr9-93829019;