rs12708283

Positions:

• chr9-108114594-C-T

Variant summary

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

The XR_007061722.1(LOC105376214):​n.721-61300G>A 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 0.262 in 151,910 control chromosomes in the GnomAD database, including 5,554 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 0.26 (5554 hom., cov: 31)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

LOC105376214 (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 (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376214	XR_007061722.1	n.721-61300G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-61300G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-61300G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39814 AN: 151794 Hom.: 5553 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.262 AC: 39826 AN: 151910 Hom.: 5554 Cov.: 31 AF XY: 0.258 AC XY: 19148 AN XY: 74250

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.285

Alfa AF: 0.274 Hom.: 1193

Bravo AF: 0.263

Asia WGS AF: 0.124 AC: 432 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	6.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12708283; hg19: chr9-110876874;