rs10984107

Positions:

• chr9-118593401-G-A

Variant summary

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

The XR_930297.2(LOC105376249):​n.163-214C>T 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 0.479 in 151,510 control chromosomes in the GnomAD database, including 19,093 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 0.48 (19093 hom., cov: 29)
• Consequence: LOC105376249 XR_930297.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

Genes affected

LOC105376249 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376249	XR_930297.2	n.163-214C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72600 AN: 151392 Hom.: 19094 Cov.: 29

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.479 AC: 72630 AN: 151510 Hom.: 19093 Cov.: 29 AF XY: 0.472 AC XY: 34963 AN XY: 74006

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.517

Alfa AF: 0.543 Hom.: 5779

Bravo AF: 0.470

Asia WGS AF: 0.235 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10984107; hg19: chr9-121355679;