3-55203710-C-T

Variant summary

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

The XR_007095917.1(LOC124906243):n.159-59788G>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 0.447 in 152,084 control chromosomes in the GnomAD database, including 16,087 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 0.45 (16087 hom., cov: 32)
• Consequence: LOC124906243 XR_007095917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

LOC124906243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906243	XR_007095917.1	n.159-59788G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68020 AN: 151966 Hom.: 16078 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.447 AC: 68049 AN: 152084 Hom.: 16087 Cov.: 32 AF XY: 0.456 AC XY: 33857 AN XY: 74308

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.449

Alfa AF: 0.453 Hom.: 14582

Bravo AF: 0.434

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.9
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510777; hg19: chr3-55237738;