rs1539143

Variant names:

• chr1-203403357-G-A
• rs1539143

Your query was ambiguous. Multiple possible variants found:

• chr1-203403357-G-A
• chr1-203403357-G-C
• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;