9-37376125-A-T

Variant names:

• chr9-37376125-A-T
• rs7031314
• XR_007061478.1:n.4376-6052A>T

Variant summary

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

The XR_007061478.1(LOC124902153):​n.4376-6052A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 150,350 control chromosomes in the GnomAD database, including 4,440 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 0.24 (4440 hom., cov: 29)
• Consequence: LOC124902153 XR_007061478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 2 publications found

Genes affected

LOC124902153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 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: 0.235 AC: 35317 AN: 150240 Hom.: 4436 Cov.: 29

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.235 AC: 35336 AN: 150350 Hom.: 4440 Cov.: 29 AF XY: 0.230 AC XY: 16828 AN XY: 73322

African (AFR) AF: 0.248 AC: 10098 AN: 40720

American (AMR) AF: 0.185 AC: 2801 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1127 AN: 3454

East Asian (EAS) AF: 0.105 AC: 537 AN: 5116

South Asian (SAS) AF: 0.264 AC: 1257 AN: 4764

European-Finnish (FIN) AF: 0.168 AC: 1698 AN: 10108

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16720 AN: 67794

Other (OTH) AF: 0.264 AC: 551 AN: 2086

Alfa AF: 0.0978 Hom.: 144

Bravo AF: 0.239

Asia WGS AF: 0.159 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
DANN	Benign	0.82
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7031314; hg19: chr9-37376122;