rs10979182

Positions:

• chr9-108054739-A-G

Variant summary

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

The XR_007061722.1(LOC105376214):​n.721-1445T>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 0.446 in 151,902 control chromosomes in the GnomAD database, including 15,733 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 0.45 (15733 hom., cov: 31)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

Genes affected

LOC105376214 (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 (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.721-1445T>C		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-1445T>C		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-1445T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67709 AN: 151782 Hom.: 15702 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.446 AC: 67797 AN: 151902 Hom.: 15733 Cov.: 31 AF XY: 0.456 AC XY: 33888 AN XY: 74236

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.458

Alfa AF: 0.425 Hom.: 1810

Bravo AF: 0.453

Asia WGS AF: 0.643 AC: 2236 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	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10979182; hg19: chr9-110817020;