rs731336

Variant names:

• chr10-44343806-T-A
• rs731336
• XR_007062369.1:n.3742+3742A>T

Variant summary

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

The XR_007062369.1(LOC124902544):​n.3742+3742A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 152,176 control chromosomes in the GnomAD database, including 145 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 0.031 (145 hom., cov: 32)
• Consequence: LOC124902544 XR_007062369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 2 publications found

Genes affected

LOC124902544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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: 0.0307 AC: 4668 AN: 152058 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0308 AC: 4680 AN: 152176 Hom.: 145 Cov.: 32 AF XY: 0.0329 AC XY: 2445 AN XY: 74394

African (AFR) AF: 0.0599 AC: 2487 AN: 41498

American (AMR) AF: 0.0146 AC: 223 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5162

South Asian (SAS) AF: 0.142 AC: 687 AN: 4822

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 836 AN: 68006

Other (OTH) AF: 0.0260 AC: 55 AN: 2112

Alfa AF: 0.0210 Hom.: 7

Bravo AF: 0.0287

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	5.3
DANN	Benign	0.89
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs731336; hg19: chr10-44839254;