rs4244145

Variant names:

• chr1-200002133-G-A
• rs4244145

Your query was ambiguous. Multiple possible variants found:

• chr1-200002133-G-A
• chr1-200002133-G-C
• chr1-200002133-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 0.834 in 152,190 control chromosomes in the GnomAD database, including 53,207 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 0.83 (53207 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.834 AC: 126838 AN: 152072 Hom.: 53175 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.834 AC: 126920 AN: 152190 Hom.: 53207 Cov.: 33 AF XY: 0.839 AC XY: 62436 AN XY: 74420

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.833

Alfa AF: 0.855 Hom.: 111561

Bravo AF: 0.832

Asia WGS AF: 0.937 AC: 3250 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.097

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4244145; hg19: chr1-199971261;