rs1516489

Positions:

• chr3-191804063-A-C

Variant summary

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

The XR_924826.2(LOC105374276):​n.103+4395T>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 0.0875 in 152,250 control chromosomes in the GnomAD database, including 751 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 0.087 (751 hom., cov: 33)
• Consequence: LOC105374276 XR_924826.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

LOC105374276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374276	XR_924826.2	n.103+4395T>G		intron_variant, non_coding_transcript_variant
LOC105374276	XR_924825.2	n.103+4395T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13313 AN: 152132 Hom.: 751 Cov.: 33

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.0875 AC: 13320 AN: 152250 Hom.: 751 Cov.: 33 AF XY: 0.0906 AC XY: 6741 AN XY: 74436

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.102 Hom.: 1013

Bravo AF: 0.0819

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.3
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1516489; hg19: chr3-191521852;