rs248471

Positions:

• chr5-141809602-G-A

Variant summary

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

The XR_001742906.2(LOC107986454):​n.9064C>T 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 0.509 in 151,864 control chromosomes in the GnomAD database, including 20,097 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 0.51 (20097 hom., cov: 31)
• Consequence: LOC107986454 XR_001742906.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LOC107986454 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986454	XR_001742906.2	n.9064C>T		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77209 AN: 151746 Hom.: 20073 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.509 AC: 77263 AN: 151864 Hom.: 20097 Cov.: 31 AF XY: 0.511 AC XY: 37879 AN XY: 74196

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.471

Alfa AF: 0.464 Hom.: 25638

Bravo AF: 0.514

Asia WGS AF: 0.519 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248471; hg19: chr5-141189168;