XR_007061902.1:n.84-3996A>T

Variant names:

• chr9-79463998-T-A
• rs7044969
• XR_007061902.1:n.84-3996A>T

Variant summary

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

The XR_007061902.1(LOC124902328):​n.84-3996A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,156 control chromosomes in the GnomAD database, including 1,319 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 0.13 (1319 hom., cov: 33)
• Consequence: LOC124902328 XR_007061902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 2 publications found

Genes affected

LOC124902328 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 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: 0.126 AC: 19225 AN: 152038 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19265 AN: 152156 Hom.: 1319 Cov.: 33 AF XY: 0.131 AC XY: 9721 AN XY: 74388

African (AFR) AF: 0.133 AC: 5539 AN: 41526

American (AMR) AF: 0.144 AC: 2196 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.134 AC: 695 AN: 5188

South Asian (SAS) AF: 0.0987 AC: 476 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10566

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7522 AN: 67998

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.122 Hom.: 145

Bravo AF: 0.126

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.54
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7044969; hg19: chr9-82078913;