rs6588313

chr1-68305601-G-Achr1-68305601-G-C

Variant summary

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

The 1-68305601-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,004 control chromosomes in the GnomAD database, including 29,800 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 0.62 (29800 hom., cov: 33)
• Consequence: LOC105378782 XR_947476.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

LOC105378782 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378782	XR_947476.3			downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94510 AN: 151886 Hom.: 29765 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.622 AC: 94592 AN: 152004 Hom.: 29800 Cov.: 33 AF XY: 0.615 AC XY: 45726 AN XY: 74298

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.619

Alfa AF: 0.535 Hom.: 2038

Bravo AF: 0.618

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.14
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6588313; hg19: chr1-68771284;