rs1539143

Positions:

• chr1-203403357-G-A
• chr1-203403357-G-T

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 0.715 in 152,122 control chromosomes in the GnomAD database, including 39,484 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 0.72 (39484 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.203403357G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108714 AN: 152004 Hom.: 39456 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.715 AC: 108795 AN: 152122 Hom.: 39484 Cov.: 32 AF XY: 0.714 AC XY: 53134 AN XY: 74368

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.722

Alfa AF: 0.756 Hom.: 90930

Bravo AF: 0.709

Asia WGS AF: 0.634 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0020
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539143; hg19: chr1-203372485;