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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.599 AC: 24822 AN: 41462

American (AMR) AF: 0.795 AC: 12148 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3039 AN: 5178

South Asian (SAS) AF: 0.644 AC: 3106 AN: 4826

European-Finnish (FIN) AF: 0.814 AC: 8609 AN: 10574

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52185 AN: 68014

Other (OTH) AF: 0.722 AC: 1525 AN: 2112

Alfa AF: 0.747 Hom.: 145582

Bravo AF: 0.709

Asia WGS AF: 0.634 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0020
DANN	Benign	0.45
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1539143; hg19: chr1-203372485;