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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.744 AC: 30880 AN: 41522

American (AMR) AF: 0.884 AC: 13493 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3468

East Asian (EAS) AF: 0.985 AC: 5110 AN: 5186

South Asian (SAS) AF: 0.932 AC: 4498 AN: 4824

European-Finnish (FIN) AF: 0.877 AC: 9292 AN: 10598

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57782 AN: 68006

Other (OTH) AF: 0.833 AC: 1760 AN: 2112

Alfa AF: 0.848 Hom.: 176164

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4244145; hg19: chr1-199971261;