rs10968093

Positions:

• chr9-27753229-G-A
• chr9-27753229-G-T

Variant summary

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

The XM_047424284.1(LOC124902135):​c.188-8221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,158 control chromosomes in the GnomAD database, including 723 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 0.067 (723 hom., cov: 32)
• Consequence: LOC124902135 XM_047424284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

Genes affected

LOC124902135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902135	XM_047424284.1	c.188-8221G>A		intron_variant			XP_047280240.1
		n.27753229G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10113 AN: 152040 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0666 AC: 10131 AN: 152158 Hom.: 723 Cov.: 32 AF XY: 0.0671 AC XY: 4988 AN XY: 74382

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0191 Hom.: 185

Bravo AF: 0.0708

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10968093; hg19: chr9-27753227;