rs3806448

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;