rs285070

Positions:

• chr13-98086511-C-A

Variant summary

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

The XR_931670.4(LOC105370328):​n.73-19465G>T 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 0.758 in 150,950 control chromosomes in the GnomAD database, including 47,748 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 0.76 (47748 hom., cov: 30)
• Consequence: LOC105370328 XR_931670.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

LOC105370328 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370328	XR_931670.4	n.73-19465G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.759 AC: 114456 AN: 150868 Hom.: 47759 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.814

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.758 AC: 114462 AN: 150950 Hom.: 47748 Cov.: 30 AF XY: 0.755 AC XY: 55701 AN XY: 73748

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.785

Alfa AF: 0.883 Hom.: 12158

Bravo AF: 0.724

Asia WGS AF: 0.625 AC: 2166 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285070; hg19: chr13-98738765;