rs952312

Positions:

• chr1-80018289-A-G

Variant summary

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

The variant allele was found at a frequency of 0.14 in 152,146 control chromosomes in the GnomAD database, including 1,889 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 0.14 (1889 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80018289A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285409	ENST00000644002.1	n.459+32257T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21288 AN: 152028 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.140 AC: 21314 AN: 152146 Hom.: 1889 Cov.: 32 AF XY: 0.144 AC XY: 10680 AN XY: 74400

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.139

Alfa AF: 0.103 Hom.: 586

Bravo AF: 0.144

Asia WGS AF: 0.236 AC: 822 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952312; hg19: chr1-80483974;