3-104555628-T-G

Variant names:

• chr3-104555628-T-G
• rs9288786
• XR_007096271.1:n.208+238A>C

Variant summary

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

The XR_007096271.1(LOC105374021):​n.208+238A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,148 control chromosomes in the GnomAD database, including 1,326 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 0.086 (1326 hom., cov: 32)
• Consequence: LOC105374021 XR_007096271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88
• Publications: 3 publications found

Genes affected

LOC105374021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13023 AN: 152030 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0857 AC: 13035 AN: 152148 Hom.: 1326 Cov.: 32 AF XY: 0.0852 AC XY: 6334 AN XY: 74370

African (AFR) AF: 0.236 AC: 9796 AN: 41466

American (AMR) AF: 0.0549 AC: 838 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3468

East Asian (EAS) AF: 0.0609 AC: 315 AN: 5170

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4824

European-Finnish (FIN) AF: 0.0120 AC: 127 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0207 AC: 1406 AN: 68024

Other (OTH) AF: 0.0745 AC: 157 AN: 2106

Alfa AF: 0.0401 Hom.: 199

Bravo AF: 0.0946

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.7
DANN	Benign	0.62
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9288786; hg19: chr3-104274472;