XR_007065730.1:n.1044+405T>G

Variant names:

• chr17-36772138-T-G
• rs295885
• XR_007065730.1:n.1044+405T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065730.1(LOC105371750):​n.1044+405T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,206 control chromosomes in the GnomAD database, including 4,696 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 0.23 (4696 hom., cov: 33)
• Consequence: LOC105371750 XR_007065730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

LOC105371750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.162).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371750	XR_007065730.1	n.1044+405T>G		intron_variant	Intron 7 of 7

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35562 AN: 152088 Hom.: 4684 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35581 AN: 152206 Hom.: 4696 Cov.: 33 AF XY: 0.235 AC XY: 17500 AN XY: 74404

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.263

Alfa AF: 0.140 Hom.: 294

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs295885; hg19: -;