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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902544	XR_007062369.1	n.3742+3742A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;