rs10979182

Variant names:

• chr9-108054739-A-G
• rs10979182
• XR_001746881.2:n.721-1445T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746881.2(LOC105376214):​n.721-1445T>C variant causes a intron 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_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 27 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.721-1445T>C		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.721-1445T>C		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.721-1445T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.398 AC: 16508 AN: 41444

American (AMR) AF: 0.598 AC: 9118 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1365 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3101 AN: 5154

South Asian (SAS) AF: 0.681 AC: 3276 AN: 4812

European-Finnish (FIN) AF: 0.472 AC: 4974 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27987 AN: 67918

Other (OTH) AF: 0.458 AC: 965 AN: 2106

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10979182; hg19: chr9-110817020;