rs2050483

Positions:

• chr14-40602267-A-C

Variant summary

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

The XR_943790.3(LOC105370466):​n.829+10096T>G 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 0.476 in 152,000 control chromosomes in the GnomAD database, including 18,357 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 0.48 (18357 hom., cov: 33)
• Consequence: LOC105370466 XR_943790.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

LOC105370466 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370466	XR_943790.3	n.829+10096T>G		intron_variant, non_coding_transcript_variant
LOC105370466	XR_943792.3	n.840-9105T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72335 AN: 151880 Hom.: 18335 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.476 AC: 72413 AN: 152000 Hom.: 18357 Cov.: 33 AF XY: 0.480 AC XY: 35653 AN XY: 74292

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.454

Alfa AF: 0.424 Hom.: 1828

Bravo AF: 0.490

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2050483; hg19: chr14-41071472;