rs3753793

Positions:

• chr1-85580205-A-C

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 0.26 in 151,686 control chromosomes in the GnomAD database, including 5,375 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 0.26 (5375 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39371 AN: 151566 Hom.: 5363 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.260 AC: 39426 AN: 151686 Hom.: 5375 Cov.: 29 AF XY: 0.262 AC XY: 19448 AN XY: 74130

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.280

Alfa AF: 0.270 Hom.: 11567

Bravo AF: 0.255

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	16
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753793; hg19: chr1-86045888;