rs9649913

Positions:

• chr8-97374280-A-G

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+44790T>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 0.694 in 152,102 control chromosomes in the GnomAD database, including 37,245 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 0.69 (37245 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+44790T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105447 AN: 151986 Hom.: 37220 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.694 AC: 105514 AN: 152102 Hom.: 37245 Cov.: 32 AF XY: 0.695 AC XY: 51662 AN XY: 74372

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.705

Alfa AF: 0.731 Hom.: 22183

Bravo AF: 0.689

Asia WGS AF: 0.527 AC: 1835 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9649913; hg19: chr8-98386508;