3-70581456-A-T

Variant summary

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

The XR_001740559.2(LOC105377152):n.210-2782T>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 0.245 in 151,778 control chromosomes in the GnomAD database, including 4,879 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 0.25 (4879 hom., cov: 31)
• Consequence: LOC105377152 XR_001740559.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

Genes affected

LOC105377152 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377152	XR_001740559.2	n.210-2782T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37183 AN: 151660 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.245 AC: 37231 AN: 151778 Hom.: 4879 Cov.: 31 AF XY: 0.250 AC XY: 18514 AN XY: 74124

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.244

Alfa AF: 0.227 Hom.: 517

Bravo AF: 0.244

Asia WGS AF: 0.447 AC: 1553 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.92
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310194; hg19: chr3-70630607;