rs1779384

chr10-44398995-C-Achr10-44398995-C-Gchr10-44398995-C-T

Variant summary

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

The XR_001747298.2(LOC107984179):n.375C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,874 control chromosomes in the GnomAD database, including 4,524 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 (4524 hom., cov: 32)
• Consequence: LOC107984179 XR_001747298.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.375C>A		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36285 AN: 151758 Hom.: 4512 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.239 AC: 36323 AN: 151874 Hom.: 4524 Cov.: 32 AF XY: 0.237 AC XY: 17559 AN XY: 74226

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.215

Alfa AF: 0.209 Hom.: 4606

Bravo AF: 0.240

Asia WGS AF: 0.249 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1779384; hg19: chr10-44894443;