rs3806448

Variant names:

• chr1-111289583-G-A
• rs3806448

Your query was ambiguous. Multiple possible variants found:

• chr1-111289583-G-A
• chr1-111289583-G-C
• chr1-111289583-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 0.458 in 152,096 control chromosomes in the GnomAD database, including 16,768 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 0.46 (16768 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.458 AC: 69552 AN: 151978 Hom.: 16758 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.458 AC: 69597 AN: 152096 Hom.: 16768 Cov.: 33 AF XY: 0.461 AC XY: 34299 AN XY: 74366

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.481

Alfa AF: 0.465 Hom.: 21397

Bravo AF: 0.471

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806448; hg19: chr1-111832205;