rs3753579

Variant names:

• chr1-11978534-G-A
• rs3753579

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 0.437 in 151,976 control chromosomes in the GnomAD database, including 15,408 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 0.44 (15408 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

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 (SAS) allele frequency at 95% confidence interval = 0.548 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: 0.437 AC: 66346 AN: 151858 Hom.: 15398 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.437 AC: 66400 AN: 151976 Hom.: 15408 Cov.: 32 AF XY: 0.444 AC XY: 32955 AN XY: 74296

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.415

Alfa AF: 0.377 Hom.: 14796

Bravo AF: 0.426

Asia WGS AF: 0.567 AC: 1968 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	0.053
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753579; hg19: chr1-12038591;