rs1904444

chr10-113317597-G-A

Variant summary

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

The XR_946329.2(LOC105378490):n.4888-3207G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,214 control chromosomes in the GnomAD database, including 1,828 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 (1828 hom., cov: 33)
• Consequence: LOC105378490 XR_946329.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

LOC105378490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378490	XR_946329.2	n.4888-3207G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20067 AN: 152096 Hom.: 1826 Cov.: 33

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.132 AC: 20070 AN: 152214 Hom.: 1828 Cov.: 33 AF XY: 0.135 AC XY: 10068 AN XY: 74412

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.135

Alfa AF: 0.152 Hom.: 2841

Bravo AF: 0.137

Asia WGS AF: 0.229 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1904444; hg19: chr10-115077356;