rs3003444

Variant names:

• chr1-17286571-T-C
• rs3003444

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 0.403 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.484 AC: 20055 AN: 41430

American (AMR) AF: 0.421 AC: 6422 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1565 AN: 5160

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4816

European-Finnish (FIN) AF: 0.348 AC: 3673 AN: 10548

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24895 AN: 67936

Other (OTH) AF: 0.427 AC: 902 AN: 2110

Alfa AF: 0.378 Hom.: 3748

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs3003444; hg19: chr1-17613066;