rs10739923

Variant names:

• chr9-91984009-T-C
• rs10739923
• XR_930124.1:n.362+1686A>G

Variant summary

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

The XR_930124.1(LOC105376148):​n.362+1686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,076 control chromosomes in the GnomAD database, including 24,667 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 0.53 (24667 hom., cov: 31)
• Consequence: LOC105376148 XR_930124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 2 publications found

Genes affected

LOC105376148 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80737 AN: 151956 Hom.: 24617 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.532 AC: 80848 AN: 152076 Hom.: 24667 Cov.: 31 AF XY: 0.531 AC XY: 39495 AN XY: 74326

African (AFR) AF: 0.847 AC: 35158 AN: 41504

American (AMR) AF: 0.567 AC: 8669 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2090 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2153 AN: 4814

European-Finnish (FIN) AF: 0.377 AC: 3991 AN: 10576

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25619 AN: 67964

Other (OTH) AF: 0.495 AC: 1045 AN: 2110

Alfa AF: 0.421 Hom.: 7574

Bravo AF: 0.558

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10739923; hg19: chr9-94746291;