rs3003444

Variant names:

• chr1-17286571-T-C
• rs3003444

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 0.403 in 151,924 control chromosomes in the GnomAD database, including 12,540 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 0.40 (12540 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 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: 0.403 AC: 61177 AN: 151806 Hom.: 12511 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.403 AC: 61254 AN: 151924 Hom.: 12540 Cov.: 31 AF XY: 0.402 AC XY: 29843 AN XY: 74240

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.427

Alfa AF: 0.379 Hom.: 2237

Bravo AF: 0.411

Asia WGS AF: 0.423 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3003444; hg19: chr1-17613066;