rs3753573

Variant names:

• chr1-185044870-G-A
• rs3753573

Your query was ambiguous. Multiple possible variants found:

• chr1-185044870-G-A
• chr1-185044870-G-C
• chr1-185044870-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 0.00691 in 152,240 control chromosomes in the GnomAD database, including 32 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 0.0069 (32 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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 = 0.0812 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: 0.00691 AC: 1051 AN: 152122 Hom.: 32 Cov.: 32

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.00478

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

GnomAD4 genome AF: 0.00691 AC: 1052 AN: 152240 Hom.: 32 Cov.: 32 AF XY: 0.00762 AC XY: 567 AN XY: 74434

Gnomad4 AFR AF: 0.00564

Gnomad4 AMR AF: 0.00373

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.0879

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00171

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00377 Hom.: 10

Bravo AF: 0.00640

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.093
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: rs3753573; hg19: chr1-185014002;