chr9-123311401-G-T

Variant names:

• chr9-123311401-G-T
• rs10739625
• XR_930331.3:n.79-5181C>A

Variant summary

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

The XR_930331.3(LOC105376265):​n.79-5181C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,116 control chromosomes in the GnomAD database, including 3,537 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 0.18 (3537 hom., cov: 32)
• Consequence: LOC105376265 XR_930331.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 4 publications found

Genes affected

LOC105376265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27360 AN: 151996 Hom.: 3528 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.180 AC: 27407 AN: 152116 Hom.: 3537 Cov.: 32 AF XY: 0.191 AC XY: 14212 AN XY: 74372

African (AFR) AF: 0.128 AC: 5298 AN: 41532

American (AMR) AF: 0.276 AC: 4208 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3784 AN: 5166

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2182 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9669 AN: 67984

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.150 Hom.: 2822

Bravo AF: 0.189

Asia WGS AF: 0.445 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.71
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10739625; hg19: chr9-126073680;