9-79465334-G-A

Variant names:

• chr9-79465334-G-A
• rs10491790
• XR_007061902.1:n.84-5332C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007061902.1(LOC124902328):​n.84-5332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,144 control chromosomes in the GnomAD database, including 3,506 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 0.14 (3506 hom., cov: 32)
• Consequence: LOC124902328 XR_007061902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 3 publications found

Genes affected

LOC124902328 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.140 AC: 21276 AN: 152026 Hom.: 3499 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.140 AC: 21314 AN: 152144 Hom.: 3506 Cov.: 32 AF XY: 0.135 AC XY: 10016 AN XY: 74398

African (AFR) AF: 0.393 AC: 16308 AN: 41452

American (AMR) AF: 0.0803 AC: 1228 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.00637 AC: 33 AN: 5178

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4826

European-Finnish (FIN) AF: 0.0171 AC: 181 AN: 10612

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3039 AN: 68010

Other (OTH) AF: 0.107 AC: 226 AN: 2108

Alfa AF: 0.0719 Hom.: 4416

Bravo AF: 0.157

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	21
DANN	Benign	0.57
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10491790; hg19: chr9-82080249;